Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/c513ad5c9b6e2827feb02c41fa8914/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/c513ad5c9b6e2827feb02c41fa8914/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6c/25a6cfefa4a0162a3041222bf0cc39/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa.fai ==> STAGING COMPLETE (5 inputs) Using GATK jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx121241M -XX:-UsePerfData -XX:ParallelGCThreads=2 -jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar MarkDuplicates --INPUT 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.md.bam --METRICS_FILE 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT 09:00:23.149 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so [Mon Jun 08 09:00:23 GMT 2026] MarkDuplicates --INPUT 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.md.bam --METRICS_FILE 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.md.bam.metrics --REMOVE_DUPLICATES false --TMP_DIR . --VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Mon Jun 08 09:00:23 GMT 2026] Executing as ?@nf-79c513ad5c9b6e2827feb02c41fa8914-e1f84-rjp25 on Linux 6.12.88 amd64; OpenJDK 64-Bit Server VM 17.0.3-internal+0-adhoc..src; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.4.0.0 INFO 2026-06-08 09:00:23 MarkDuplicates Start of doWork freeMemory: 105130992; totalMemory: 134217728; maxMemory: 127137742848 INFO 2026-06-08 09:00:23 MarkDuplicates Reading input file and constructing read end information. INFO 2026-06-08 09:00:23 MarkDuplicates Will retain up to 460643995 data points before spilling to disk. INFO 2026-06-08 09:00:28 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: chr1:1,387,345 INFO 2026-06-08 09:00:28 MarkDuplicates Tracking 3583 as yet unmatched pairs. 418 records in RAM. INFO 2026-06-08 09:00:30 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 2s. Last read position: chr1:2,519,787 INFO 2026-06-08 09:00:30 MarkDuplicates Tracking 6210 as yet unmatched pairs. 24 records in RAM. INFO 2026-06-08 09:00:32 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 2s. Last read position: chr1:8,358,754 INFO 2026-06-08 09:00:32 MarkDuplicates Tracking 9659 as yet unmatched pairs. 205 records in RAM. INFO 2026-06-08 09:00:35 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 2s. Last read position: chr1:11,055,827 INFO 2026-06-08 09:00:35 MarkDuplicates Tracking 12600 as yet unmatched pairs. 198 records in RAM. INFO 2026-06-08 09:00:37 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: chr1:13,782,384 INFO 2026-06-08 09:00:37 MarkDuplicates Tracking 15344 as yet unmatched pairs. 129 records in RAM. INFO 2026-06-08 09:00:39 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 2s. Last read position: chr1:16,582,620 INFO 2026-06-08 09:00:39 MarkDuplicates Tracking 18337 as yet unmatched pairs. 511 records in RAM. INFO 2026-06-08 09:00:41 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 2s. Last read position: chr1:19,183,857 INFO 2026-06-08 09:00:41 MarkDuplicates Tracking 21244 as yet unmatched pairs. 457 records in RAM. INFO 2026-06-08 09:00:43 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 1s. Last read position: chr1:21,824,568 INFO 2026-06-08 09:00:43 MarkDuplicates Tracking 23714 as yet unmatched pairs. 106 records in RAM. INFO 2026-06-08 09:00:45 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 1s. Last read position: chr1:23,361,955 INFO 2026-06-08 09:00:45 MarkDuplicates Tracking 26625 as yet unmatched pairs. 139 records in RAM. INFO 2026-06-08 09:00:48 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 2s. Last read position: chr1:25,563,117 INFO 2026-06-08 09:00:48 MarkDuplicates Tracking 29290 as yet unmatched pairs. 73 records in RAM. INFO 2026-06-08 09:00:51 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 2s. Last read position: chr1:26,774,849 INFO 2026-06-08 09:00:51 MarkDuplicates Tracking 32380 as yet unmatched pairs. 365 records in RAM. INFO 2026-06-08 09:00:53 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 2s. Last read position: chr1:28,714,095 INFO 2026-06-08 09:00:53 MarkDuplicates Tracking 35108 as yet unmatched pairs. 239 records in RAM. INFO 2026-06-08 09:00:55 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 2s. Last read position: chr1:31,700,036 INFO 2026-06-08 09:00:55 MarkDuplicates Tracking 38754 as yet unmatched pairs. 964 records in RAM. INFO 2026-06-08 09:00:58 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 2s. Last read position: chr1:33,281,593 INFO 2026-06-08 09:00:58 MarkDuplicates Tracking 40999 as yet unmatched pairs. 190 records in RAM. INFO 2026-06-08 09:01:01 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 3s. Last read position: chr1:35,449,891 INFO 2026-06-08 09:01:01 MarkDuplicates Tracking 44155 as yet unmatched pairs. 154 records in RAM. INFO 2026-06-08 09:01:04 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 2s. Last read position: chr1:37,989,558 INFO 2026-06-08 09:01:04 MarkDuplicates Tracking 47241 as yet unmatched pairs. 401 records in RAM. INFO 2026-06-08 09:01:06 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 2s. Last read position: chr1:39,841,782 INFO 2026-06-08 09:01:06 MarkDuplicates Tracking 49795 as yet unmatched pairs. 205 records in RAM. INFO 2026-06-08 09:01:08 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 2s. Last read position: chr1:43,441,763 INFO 2026-06-08 09:01:08 MarkDuplicates Tracking 52673 as yet unmatched pairs. 145 records in RAM. INFO 2026-06-08 09:01:10 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 2s. Last read position: chr1:44,827,621 INFO 2026-06-08 09:01:10 MarkDuplicates Tracking 56524 as yet unmatched pairs. 785 records in RAM. INFO 2026-06-08 09:01:13 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 2s. Last read position: chr1:46,034,222 INFO 2026-06-08 09:01:13 MarkDuplicates Tracking 58986 as yet unmatched pairs. 305 records in RAM. INFO 2026-06-08 09:01:15 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 2s. Last read position: chr1:52,033,067 INFO 2026-06-08 09:01:15 MarkDuplicates Tracking 61829 as yet unmatched pairs. 138 records in RAM. INFO 2026-06-08 09:01:17 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 2s. Last read position: chr1:56,524,446 INFO 2026-06-08 09:01:17 MarkDuplicates Tracking 64603 as yet unmatched pairs. 155 records in RAM. INFO 2026-06-08 09:01:19 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 1s. Last read position: chr1:62,583,200 INFO 2026-06-08 09:01:19 MarkDuplicates Tracking 67793 as yet unmatched pairs. 262 records in RAM. INFO 2026-06-08 09:01:21 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 2s. Last read position: chr1:74,205,293 INFO 2026-06-08 09:01:21 MarkDuplicates Tracking 70313 as yet unmatched pairs. 179 records in RAM. INFO 2026-06-08 09:01:23 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 2s. Last read position: chr1:85,582,255 INFO 2026-06-08 09:01:23 MarkDuplicates Tracking 73853 as yet unmatched pairs. 1068 records in RAM. INFO 2026-06-08 09:01:25 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 2s. Last read position: chr1:92,833,547 INFO 2026-06-08 09:01:25 MarkDuplicates Tracking 75957 as yet unmatched pairs. 440 records in RAM. INFO 2026-06-08 09:01:27 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 2s. Last read position: chr1:100,720,608 INFO 2026-06-08 09:01:27 MarkDuplicates Tracking 78337 as yet unmatched pairs. 158 records in RAM. INFO 2026-06-08 09:01:29 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 1s. Last read position: chr1:110,018,619 INFO 2026-06-08 09:01:29 MarkDuplicates Tracking 80726 as yet unmatched pairs. 178 records in RAM. INFO 2026-06-08 09:01:32 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 2s. Last read position: chr1:113,766,108 INFO 2026-06-08 09:01:32 MarkDuplicates Tracking 83593 as yet unmatched pairs. 209 records in RAM. INFO 2026-06-08 09:01:34 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 2s. Last read position: chr1:116,961,415 INFO 2026-06-08 09:01:34 MarkDuplicates Tracking 86356 as yet unmatched pairs. 170 records in RAM. INFO 2026-06-08 09:01:36 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 2s. Last read position: chr1:119,916,645 INFO 2026-06-08 09:01:36 MarkDuplicates Tracking 90325 as yet unmatched pairs. 1244 records in RAM. INFO 2026-06-08 09:01:38 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 2s. Last read position: chr1:119,967,498 INFO 2026-06-08 09:01:38 MarkDuplicates Tracking 92951 as yet unmatched pairs. 983 records in RAM. INFO 2026-06-08 09:01:40 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 1s. Last read position: chr1:120,805,734 INFO 2026-06-08 09:01:40 MarkDuplicates Tracking 93873 as yet unmatched pairs. 250 records in RAM. INFO 2026-06-08 09:01:42 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 1s. Last read position: chr1:145,374,071 INFO 2026-06-08 09:01:42 MarkDuplicates Tracking 94961 as yet unmatched pairs. 138 records in RAM. INFO 2026-06-08 09:01:44 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 1s. Last read position: chr1:146,101,859 INFO 2026-06-08 09:01:44 MarkDuplicates Tracking 96353 as yet unmatched pairs. 136 records in RAM. INFO 2026-06-08 09:01:45 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 1s. Last read position: chr1:146,963,131 INFO 2026-06-08 09:01:45 MarkDuplicates Tracking 97374 as yet unmatched pairs. 219 records in RAM. INFO 2026-06-08 09:01:47 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 1s. Last read position: chr1:148,540,183 INFO 2026-06-08 09:01:47 MarkDuplicates Tracking 99264 as yet unmatched pairs. 655 records in RAM. INFO 2026-06-08 09:01:48 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 1s. Last read position: chr1:148,589,323 INFO 2026-06-08 09:01:48 MarkDuplicates Tracking 99232 as yet unmatched pairs. 246 records in RAM. INFO 2026-06-08 09:01:50 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 1s. Last read position: chr1:149,455,457 INFO 2026-06-08 09:01:50 MarkDuplicates Tracking 100786 as yet unmatched pairs. 407 records in RAM. INFO 2026-06-08 09:01:52 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 1s. Last read position: chr1:149,886,425 INFO 2026-06-08 09:01:52 MarkDuplicates Tracking 101943 as yet unmatched pairs. 327 records in RAM. INFO 2026-06-08 09:01:53 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 1s. Last read position: chr1:150,816,368 INFO 2026-06-08 09:01:53 MarkDuplicates Tracking 104551 as yet unmatched pairs. 155 records in RAM. INFO 2026-06-08 09:01:56 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 2s. Last read position: chr1:151,612,423 INFO 2026-06-08 09:01:56 MarkDuplicates Tracking 107474 as yet unmatched pairs. 207 records in RAM. INFO 2026-06-08 09:01:58 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 2s. Last read position: chr1:154,172,012 INFO 2026-06-08 09:01:58 MarkDuplicates Tracking 110716 as yet unmatched pairs. 831 records in RAM. INFO 2026-06-08 09:02:00 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 2s. Last read position: chr1:154,968,003 INFO 2026-06-08 09:02:00 MarkDuplicates Tracking 113158 as yet unmatched pairs. 599 records in RAM. INFO 2026-06-08 09:02:02 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 2s. Last read position: chr1:155,670,395 INFO 2026-06-08 09:02:02 MarkDuplicates Tracking 115300 as yet unmatched pairs. 257 records in RAM. INFO 2026-06-08 09:02:04 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 1s. Last read position: chr1:156,136,212 INFO 2026-06-08 09:02:04 MarkDuplicates Tracking 118247 as yet unmatched pairs. 138 records in RAM. INFO 2026-06-08 09:02:06 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 2s. Last read position: chr1:156,745,040 INFO 2026-06-08 09:02:06 MarkDuplicates Tracking 121296 as yet unmatched pairs. 271 records in RAM. INFO 2026-06-08 09:02:08 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 2s. Last read position: chr1:160,123,313 INFO 2026-06-08 09:02:08 MarkDuplicates Tracking 124004 as yet unmatched pairs. 97 records in RAM. INFO 2026-06-08 09:02:10 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 2s. Last read position: chr1:162,023,366 INFO 2026-06-08 09:02:10 MarkDuplicates Tracking 126684 as yet unmatched pairs. 110 records in RAM. INFO 2026-06-08 09:02:13 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:01:47s. Time for last 1,000,000: 2s. Last read position: chr1:171,524,920 INFO 2026-06-08 09:02:13 MarkDuplicates Tracking 129723 as yet unmatched pairs. 405 records in RAM. INFO 2026-06-08 09:02:15 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 2s. Last read position: chr1:173,873,484 INFO 2026-06-08 09:02:15 MarkDuplicates Tracking 132016 as yet unmatched pairs. 143 records in RAM. INFO 2026-06-08 09:02:18 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 2s. Last read position: chr1:182,842,603 INFO 2026-06-08 09:02:18 MarkDuplicates Tracking 134886 as yet unmatched pairs. 115 records in RAM. INFO 2026-06-08 09:02:20 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 2s. Last read position: chr1:186,320,369 INFO 2026-06-08 09:02:20 MarkDuplicates Tracking 138248 as yet unmatched pairs. 766 records in RAM. INFO 2026-06-08 09:02:23 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 2s. Last read position: chr1:193,122,202 INFO 2026-06-08 09:02:23 MarkDuplicates Tracking 139986 as yet unmatched pairs. 107 records in RAM. INFO 2026-06-08 09:02:25 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 2s. Last read position: chr1:201,215,633 INFO 2026-06-08 09:02:25 MarkDuplicates Tracking 142483 as yet unmatched pairs. 66 records in RAM. INFO 2026-06-08 09:02:27 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 2s. Last read position: chr1:203,799,656 INFO 2026-06-08 09:02:27 MarkDuplicates Tracking 145620 as yet unmatched pairs. 440 records in RAM. INFO 2026-06-08 09:02:30 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 2s. Last read position: chr1:205,718,228 INFO 2026-06-08 09:02:30 MarkDuplicates Tracking 148365 as yet unmatched pairs. 535 records in RAM. INFO 2026-06-08 09:02:32 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 2s. Last read position: chr1:212,951,785 INFO 2026-06-08 09:02:32 MarkDuplicates Tracking 150452 as yet unmatched pairs. 109 records in RAM. INFO 2026-06-08 09:02:34 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 2s. Last read position: chr1:222,629,797 INFO 2026-06-08 09:02:34 MarkDuplicates Tracking 153020 as yet unmatched pairs. 116 records in RAM. INFO 2026-06-08 09:02:37 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 2s. Last read position: chr1:225,856,955 INFO 2026-06-08 09:02:37 MarkDuplicates Tracking 155564 as yet unmatched pairs. 74 records in RAM. INFO 2026-06-08 09:02:39 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 2s. Last read position: chr1:228,306,875 INFO 2026-06-08 09:02:39 MarkDuplicates Tracking 158642 as yet unmatched pairs. 46 records in RAM. INFO 2026-06-08 09:02:41 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 2s. Last read position: chr1:234,608,541 INFO 2026-06-08 09:02:41 MarkDuplicates Tracking 162152 as yet unmatched pairs. 257 records in RAM. INFO 2026-06-08 09:02:45 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 3s. Last read position: chr1:243,341,063 INFO 2026-06-08 09:02:45 MarkDuplicates Tracking 164745 as yet unmatched pairs. 58 records in RAM. INFO 2026-06-08 09:02:49 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 4s. Last read position: chr2:218,920 INFO 2026-06-08 09:02:49 MarkDuplicates Tracking 167584 as yet unmatched pairs. 162924 records in RAM. INFO 2026-06-08 09:02:51 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:02:25s. Time for last 1,000,000: 1s. Last read position: chr2:9,436,333 INFO 2026-06-08 09:02:51 MarkDuplicates Tracking 170692 as yet unmatched pairs. 165930 records in RAM. INFO 2026-06-08 09:02:53 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 2s. Last read position: chr2:17,760,007 INFO 2026-06-08 09:02:53 MarkDuplicates Tracking 173438 as yet unmatched pairs. 168569 records in RAM. INFO 2026-06-08 09:02:55 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 2s. Last read position: chr2:24,707,349 INFO 2026-06-08 09:02:55 MarkDuplicates Tracking 176701 as yet unmatched pairs. 171728 records in RAM. INFO 2026-06-08 09:02:57 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 2s. Last read position: chr2:27,080,867 INFO 2026-06-08 09:02:57 MarkDuplicates Tracking 179222 as yet unmatched pairs. 174169 records in RAM. INFO 2026-06-08 09:02:59 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 2s. Last read position: chr2:27,653,682 INFO 2026-06-08 09:02:59 MarkDuplicates Tracking 182676 as yet unmatched pairs. 177574 records in RAM. INFO 2026-06-08 09:03:01 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,253 INFO 2026-06-08 09:03:01 MarkDuplicates Tracking 233383 as yet unmatched pairs. 177338 records in RAM. INFO 2026-06-08 09:03:03 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,264 INFO 2026-06-08 09:03:03 MarkDuplicates Tracking 334705 as yet unmatched pairs. 172243 records in RAM. INFO 2026-06-08 09:03:06 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,264 INFO 2026-06-08 09:03:06 MarkDuplicates Tracking 977251 as yet unmatched pairs. 138558 records in RAM. INFO 2026-06-08 09:03:08 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,404 INFO 2026-06-08 09:03:08 MarkDuplicates Tracking 1444138 as yet unmatched pairs. 114062 records in RAM. INFO 2026-06-08 09:03:10 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,406 INFO 2026-06-08 09:03:10 MarkDuplicates Tracking 1451787 as yet unmatched pairs. 113713 records in RAM. INFO 2026-06-08 09:03:12 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,452 INFO 2026-06-08 09:03:12 MarkDuplicates Tracking 1554428 as yet unmatched pairs. 108464 records in RAM. INFO 2026-06-08 09:03:13 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 1s. Last read position: chr2:38,749,623 INFO 2026-06-08 09:03:13 MarkDuplicates Tracking 1554833 as yet unmatched pairs. 105831 records in RAM. INFO 2026-06-08 09:03:15 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 1s. Last read position: chr2:42,579,105 INFO 2026-06-08 09:03:15 MarkDuplicates Tracking 1552214 as yet unmatched pairs. 103112 records in RAM. INFO 2026-06-08 09:03:17 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 2s. Last read position: chr2:45,652,150 INFO 2026-06-08 09:03:17 MarkDuplicates Tracking 1549071 as yet unmatched pairs. 99878 records in RAM. INFO 2026-06-08 09:03:20 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:02:54s. Time for last 1,000,000: 2s. Last read position: chr2:54,622,395 INFO 2026-06-08 09:03:20 MarkDuplicates Tracking 1546844 as yet unmatched pairs. 97480 records in RAM. INFO 2026-06-08 09:03:22 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 1s. Last read position: chr2:55,317,818 INFO 2026-06-08 09:03:22 MarkDuplicates Tracking 1544871 as yet unmatched pairs. 95442 records in RAM. INFO 2026-06-08 09:03:23 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 1s. Last read position: chr2:61,394,943 INFO 2026-06-08 09:03:23 MarkDuplicates Tracking 1541517 as yet unmatched pairs. 92007 records in RAM. INFO 2026-06-08 09:03:25 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 2s. Last read position: chr2:68,046,005 INFO 2026-06-08 09:03:25 MarkDuplicates Tracking 1539216 as yet unmatched pairs. 89603 records in RAM. INFO 2026-06-08 09:03:28 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:03:02s. Time for last 1,000,000: 2s. Last read position: chr2:70,288,088 INFO 2026-06-08 09:03:28 MarkDuplicates Tracking 1536762 as yet unmatched pairs. 87051 records in RAM. INFO 2026-06-08 09:03:29 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 1s. Last read position: chr2:73,601,309 INFO 2026-06-08 09:03:29 MarkDuplicates Tracking 1534100 as yet unmatched pairs. 84293 records in RAM. INFO 2026-06-08 09:03:32 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 2s. Last read position: chr2:84,906,075 INFO 2026-06-08 09:03:32 MarkDuplicates Tracking 1531739 as yet unmatched pairs. 81873 records in RAM. INFO 2026-06-08 09:03:34 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 2s. Last read position: chr2:86,987,235 INFO 2026-06-08 09:03:34 MarkDuplicates Tracking 1528770 as yet unmatched pairs. 78860 records in RAM. INFO 2026-06-08 09:03:36 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 2s. Last read position: chr2:96,289,347 INFO 2026-06-08 09:03:36 MarkDuplicates Tracking 1527204 as yet unmatched pairs. 77165 records in RAM. INFO 2026-06-08 09:03:38 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 2s. Last read position: chr2:99,195,681 INFO 2026-06-08 09:03:38 MarkDuplicates Tracking 1524559 as yet unmatched pairs. 74447 records in RAM. INFO 2026-06-08 09:03:41 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:03:15s. Time for last 1,000,000: 2s. Last read position: chr2:106,129,721 INFO 2026-06-08 09:03:41 MarkDuplicates Tracking 1522027 as yet unmatched pairs. 71798 records in RAM. INFO 2026-06-08 09:03:42 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 1s. Last read position: chr2:108,764,300 INFO 2026-06-08 09:03:42 MarkDuplicates Tracking 1520963 as yet unmatched pairs. 70680 records in RAM. INFO 2026-06-08 09:03:44 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 1s. Last read position: chr2:109,836,204 INFO 2026-06-08 09:03:44 MarkDuplicates Tracking 1519021 as yet unmatched pairs. 68673 records in RAM. INFO 2026-06-08 09:03:46 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:03:20s. Time for last 1,000,000: 1s. Last read position: chr2:112,388,626 INFO 2026-06-08 09:03:46 MarkDuplicates Tracking 1517555 as yet unmatched pairs. 67149 records in RAM. INFO 2026-06-08 09:03:47 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:03:21s. Time for last 1,000,000: 1s. Last read position: chr2:120,970,467 INFO 2026-06-08 09:03:47 MarkDuplicates Tracking 1515982 as yet unmatched pairs. 65488 records in RAM. INFO 2026-06-08 09:03:49 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:03:23s. Time for last 1,000,000: 2s. Last read position: chr2:127,999,818 INFO 2026-06-08 09:03:49 MarkDuplicates Tracking 1513145 as yet unmatched pairs. 62546 records in RAM. INFO 2026-06-08 09:03:51 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:03:25s. Time for last 1,000,000: 1s. Last read position: chr2:135,933,910 INFO 2026-06-08 09:03:51 MarkDuplicates Tracking 1510661 as yet unmatched pairs. 59960 records in RAM. INFO 2026-06-08 09:03:53 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:03:27s. Time for last 1,000,000: 2s. Last read position: chr2:151,631,248 INFO 2026-06-08 09:03:53 MarkDuplicates Tracking 1508253 as yet unmatched pairs. 57453 records in RAM. INFO 2026-06-08 09:03:55 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:03:29s. Time for last 1,000,000: 2s. Last read position: chr2:159,438,428 INFO 2026-06-08 09:03:55 MarkDuplicates Tracking 1506156 as yet unmatched pairs. 55241 records in RAM. INFO 2026-06-08 09:03:57 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:03:31s. Time for last 1,000,000: 1s. Last read position: chr2:170,859,757 INFO 2026-06-08 09:03:57 MarkDuplicates Tracking 1503449 as yet unmatched pairs. 52426 records in RAM. INFO 2026-06-08 09:03:59 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 1s. Last read position: chr2:175,114,708 INFO 2026-06-08 09:03:59 MarkDuplicates Tracking 1501220 as yet unmatched pairs. 50132 records in RAM. INFO 2026-06-08 09:04:01 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:03:35s. Time for last 1,000,000: 2s. Last read position: chr2:178,621,574 INFO 2026-06-08 09:04:01 MarkDuplicates Tracking 1498509 as yet unmatched pairs. 47337 records in RAM. INFO 2026-06-08 09:04:03 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 2s. Last read position: chr2:188,990,317 INFO 2026-06-08 09:04:03 MarkDuplicates Tracking 1496620 as yet unmatched pairs. 45299 records in RAM. INFO 2026-06-08 09:04:05 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:03:39s. Time for last 1,000,000: 1s. Last read position: chr2:189,005,359 INFO 2026-06-08 09:04:05 MarkDuplicates Tracking 1493685 as yet unmatched pairs. 42319 records in RAM. INFO 2026-06-08 09:04:08 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:03:42s. Time for last 1,000,000: 2s. Last read position: chr2:189,078,515 INFO 2026-06-08 09:04:08 MarkDuplicates Tracking 1490712 as yet unmatched pairs. 39280 records in RAM. INFO 2026-06-08 09:04:10 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:03:44s. Time for last 1,000,000: 2s. Last read position: chr2:196,792,961 INFO 2026-06-08 09:04:10 MarkDuplicates Tracking 1487050 as yet unmatched pairs. 35527 records in RAM. INFO 2026-06-08 09:04:12 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:03:46s. Time for last 1,000,000: 1s. Last read position: chr2:201,140,359 INFO 2026-06-08 09:04:12 MarkDuplicates Tracking 1484860 as yet unmatched pairs. 33252 records in RAM. INFO 2026-06-08 09:04:14 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:03:48s. Time for last 1,000,000: 2s. Last read position: chr2:205,372,859 INFO 2026-06-08 09:04:14 MarkDuplicates Tracking 1482288 as yet unmatched pairs. 30564 records in RAM. INFO 2026-06-08 09:04:16 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:03:50s. Time for last 1,000,000: 2s. Last read position: chr2:215,361,563 INFO 2026-06-08 09:04:16 MarkDuplicates Tracking 1481440 as yet unmatched pairs. 29631 records in RAM. INFO 2026-06-08 09:04:18 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:03:52s. Time for last 1,000,000: 1s. Last read position: chr2:215,379,248 INFO 2026-06-08 09:04:18 MarkDuplicates Tracking 1478163 as yet unmatched pairs. 26330 records in RAM. INFO 2026-06-08 09:04:20 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:03:54s. Time for last 1,000,000: 2s. Last read position: chr2:215,407,178 INFO 2026-06-08 09:04:20 MarkDuplicates Tracking 1476672 as yet unmatched pairs. 24802 records in RAM. INFO 2026-06-08 09:04:22 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 2s. Last read position: chr2:215,435,723 INFO 2026-06-08 09:04:22 MarkDuplicates Tracking 1472545 as yet unmatched pairs. 20648 records in RAM. INFO 2026-06-08 09:04:23 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:03:57s. Time for last 1,000,000: 1s. Last read position: chr2:218,643,519 INFO 2026-06-08 09:04:23 MarkDuplicates Tracking 1469498 as yet unmatched pairs. 17528 records in RAM. INFO 2026-06-08 09:04:25 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:03:59s. Time for last 1,000,000: 2s. Last read position: chr2:222,634,400 INFO 2026-06-08 09:04:25 MarkDuplicates Tracking 1466269 as yet unmatched pairs. 14222 records in RAM. INFO 2026-06-08 09:04:27 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 2s. Last read position: chr2:231,456,033 INFO 2026-06-08 09:04:27 MarkDuplicates Tracking 1463940 as yet unmatched pairs. 11737 records in RAM. INFO 2026-06-08 09:04:29 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:04:03s. Time for last 1,000,000: 1s. Last read position: chr2:233,438,216 INFO 2026-06-08 09:04:29 MarkDuplicates Tracking 1461042 as yet unmatched pairs. 8773 records in RAM. INFO 2026-06-08 09:04:32 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:04:06s. Time for last 1,000,000: 2s. Last read position: chr2:237,366,711 INFO 2026-06-08 09:04:32 MarkDuplicates Tracking 1458429 as yet unmatched pairs. 6087 records in RAM. INFO 2026-06-08 09:04:34 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:04:08s. Time for last 1,000,000: 1s. Last read position: chr2:239,961,078 INFO 2026-06-08 09:04:34 MarkDuplicates Tracking 1455440 as yet unmatched pairs. 2994 records in RAM. INFO 2026-06-08 09:04:36 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:04:10s. Time for last 1,000,000: 2s. Last read position: chr3:3,845,598 INFO 2026-06-08 09:04:36 MarkDuplicates Tracking 1452361 as yet unmatched pairs. 69264 records in RAM. INFO 2026-06-08 09:04:39 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:04:13s. Time for last 1,000,000: 2s. Last read position: chr3:9,475,637 INFO 2026-06-08 09:04:39 MarkDuplicates Tracking 1449927 as yet unmatched pairs. 66725 records in RAM. INFO 2026-06-08 09:04:41 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 2s. Last read position: chr3:12,587,593 INFO 2026-06-08 09:04:41 MarkDuplicates Tracking 1447123 as yet unmatched pairs. 63816 records in RAM. INFO 2026-06-08 09:04:42 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:04:16s. Time for last 1,000,000: 1s. Last read position: chr3:15,432,199 INFO 2026-06-08 09:04:42 MarkDuplicates Tracking 1444135 as yet unmatched pairs. 60759 records in RAM. INFO 2026-06-08 09:04:44 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:04:18s. Time for last 1,000,000: 2s. Last read position: chr3:27,431,471 INFO 2026-06-08 09:04:44 MarkDuplicates Tracking 1442047 as yet unmatched pairs. 58506 records in RAM. INFO 2026-06-08 09:04:46 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:04:20s. Time for last 1,000,000: 2s. Last read position: chr3:37,251,343 INFO 2026-06-08 09:04:46 MarkDuplicates Tracking 1439238 as yet unmatched pairs. 55586 records in RAM. INFO 2026-06-08 09:04:48 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:04:22s. Time for last 1,000,000: 1s. Last read position: chr3:41,224,019 INFO 2026-06-08 09:04:48 MarkDuplicates Tracking 1437154 as yet unmatched pairs. 53438 records in RAM. INFO 2026-06-08 09:04:50 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:04:24s. Time for last 1,000,000: 1s. Last read position: chr3:45,085,828 INFO 2026-06-08 09:04:50 MarkDuplicates Tracking 1434135 as yet unmatched pairs. 50349 records in RAM. INFO 2026-06-08 09:04:52 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 2s. Last read position: chr3:47,680,488 INFO 2026-06-08 09:04:52 MarkDuplicates Tracking 1431450 as yet unmatched pairs. 47605 records in RAM. INFO 2026-06-08 09:04:54 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 1s. Last read position: chr3:49,011,707 INFO 2026-06-08 09:04:54 MarkDuplicates Tracking 1428764 as yet unmatched pairs. 44844 records in RAM. INFO 2026-06-08 09:04:57 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:04:31s. Time for last 1,000,000: 2s. Last read position: chr3:49,358,084 INFO 2026-06-08 09:04:57 MarkDuplicates Tracking 1425535 as yet unmatched pairs. 41570 records in RAM. INFO 2026-06-08 09:04:59 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:04:33s. Time for last 1,000,000: 2s. Last read position: chr3:50,297,386 INFO 2026-06-08 09:04:59 MarkDuplicates Tracking 1422794 as yet unmatched pairs. 38772 records in RAM. INFO 2026-06-08 09:05:01 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:04:35s. Time for last 1,000,000: 2s. Last read position: chr3:52,370,211 INFO 2026-06-08 09:05:01 MarkDuplicates Tracking 1419845 as yet unmatched pairs. 35772 records in RAM. INFO 2026-06-08 09:05:03 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:04:37s. Time for last 1,000,000: 1s. Last read position: chr3:53,228,303 INFO 2026-06-08 09:05:03 MarkDuplicates Tracking 1416936 as yet unmatched pairs. 32805 records in RAM. INFO 2026-06-08 09:05:05 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:04:39s. Time for last 1,000,000: 2s. Last read position: chr3:61,671,265 INFO 2026-06-08 09:05:05 MarkDuplicates Tracking 1414462 as yet unmatched pairs. 30207 records in RAM. INFO 2026-06-08 09:05:07 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:04:41s. Time for last 1,000,000: 2s. Last read position: chr3:69,055,489 INFO 2026-06-08 09:05:07 MarkDuplicates Tracking 1412074 as yet unmatched pairs. 27682 records in RAM. INFO 2026-06-08 09:05:09 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:04:43s. Time for last 1,000,000: 1s. Last read position: chr3:97,879,983 INFO 2026-06-08 09:05:09 MarkDuplicates Tracking 1409434 as yet unmatched pairs. 24902 records in RAM. INFO 2026-06-08 09:05:11 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:04:45s. Time for last 1,000,000: 2s. Last read position: chr3:113,250,712 INFO 2026-06-08 09:05:11 MarkDuplicates Tracking 1407112 as yet unmatched pairs. 22496 records in RAM. INFO 2026-06-08 09:05:12 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:04:46s. Time for last 1,000,000: 1s. Last read position: chr3:122,923,696 INFO 2026-06-08 09:05:12 MarkDuplicates Tracking 1404374 as yet unmatched pairs. 19668 records in RAM. INFO 2026-06-08 09:05:14 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:04:48s. Time for last 1,000,000: 2s. Last read position: chr3:129,556,616 INFO 2026-06-08 09:05:14 MarkDuplicates Tracking 1401425 as yet unmatched pairs. 16623 records in RAM. INFO 2026-06-08 09:05:17 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:04:51s. Time for last 1,000,000: 2s. Last read position: chr3:141,553,845 INFO 2026-06-08 09:05:17 MarkDuplicates Tracking 1398745 as yet unmatched pairs. 13832 records in RAM. INFO 2026-06-08 09:05:19 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:04:53s. Time for last 1,000,000: 2s. Last read position: chr3:150,572,495 INFO 2026-06-08 09:05:19 MarkDuplicates Tracking 1395961 as yet unmatched pairs. 10968 records in RAM. INFO 2026-06-08 09:05:21 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:04:55s. Time for last 1,000,000: 2s. Last read position: chr3:171,713,933 INFO 2026-06-08 09:05:21 MarkDuplicates Tracking 1393671 as yet unmatched pairs. 8564 records in RAM. INFO 2026-06-08 09:05:23 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:04:57s. Time for last 1,000,000: 2s. Last read position: chr3:184,321,764 INFO 2026-06-08 09:05:23 MarkDuplicates Tracking 1391105 as yet unmatched pairs. 5875 records in RAM. INFO 2026-06-08 09:05:25 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:04:59s. Time for last 1,000,000: 1s. Last read position: chr3:194,136,987 INFO 2026-06-08 09:05:25 MarkDuplicates Tracking 1388553 as yet unmatched pairs. 3269 records in RAM. INFO 2026-06-08 09:05:27 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:05:01s. Time for last 1,000,000: 1s. Last read position: chr3:196,472,647 INFO 2026-06-08 09:05:27 MarkDuplicates Tracking 1386081 as yet unmatched pairs. 766 records in RAM. INFO 2026-06-08 09:05:29 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:05:03s. Time for last 1,000,000: 2s. Last read position: chr4:1,171,302 INFO 2026-06-08 09:05:29 MarkDuplicates Tracking 1383387 as yet unmatched pairs. 55291 records in RAM. INFO 2026-06-08 09:05:31 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:05:05s. Time for last 1,000,000: 1s. Last read position: chr4:2,830,086 INFO 2026-06-08 09:05:31 MarkDuplicates Tracking 1380142 as yet unmatched pairs. 51985 records in RAM. INFO 2026-06-08 09:05:33 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 2s. Last read position: chr4:7,060,939 INFO 2026-06-08 09:05:33 MarkDuplicates Tracking 1377156 as yet unmatched pairs. 48922 records in RAM. INFO 2026-06-08 09:05:35 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 1s. Last read position: chr4:13,601,037 INFO 2026-06-08 09:05:35 MarkDuplicates Tracking 1374719 as yet unmatched pairs. 46395 records in RAM. INFO 2026-06-08 09:05:37 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:05:11s. Time for last 1,000,000: 1s. Last read position: chr4:24,570,715 INFO 2026-06-08 09:05:37 MarkDuplicates Tracking 1372509 as yet unmatched pairs. 44058 records in RAM. INFO 2026-06-08 09:05:39 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:05:13s. Time for last 1,000,000: 2s. Last read position: chr4:39,825,470 INFO 2026-06-08 09:05:39 MarkDuplicates Tracking 1369595 as yet unmatched pairs. 41077 records in RAM. INFO 2026-06-08 09:05:41 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:05:15s. Time for last 1,000,000: 2s. Last read position: chr4:53,383,819 INFO 2026-06-08 09:05:41 MarkDuplicates Tracking 1367200 as yet unmatched pairs. 38572 records in RAM. INFO 2026-06-08 09:05:43 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:05:17s. Time for last 1,000,000: 1s. Last read position: chr4:56,988,134 INFO 2026-06-08 09:05:43 MarkDuplicates Tracking 1364575 as yet unmatched pairs. 35875 records in RAM. INFO 2026-06-08 09:05:45 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:05:19s. Time for last 1,000,000: 2s. Last read position: chr4:73,142,653 INFO 2026-06-08 09:05:45 MarkDuplicates Tracking 1362021 as yet unmatched pairs. 33249 records in RAM. INFO 2026-06-08 09:05:47 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:05:21s. Time for last 1,000,000: 1s. Last read position: chr4:78,911,951 INFO 2026-06-08 09:05:47 MarkDuplicates Tracking 1359416 as yet unmatched pairs. 30528 records in RAM. INFO 2026-06-08 09:05:49 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:05:23s. Time for last 1,000,000: 2s. Last read position: chr4:84,860,417 INFO 2026-06-08 09:05:49 MarkDuplicates Tracking 1356972 as yet unmatched pairs. 28015 records in RAM. INFO 2026-06-08 09:05:51 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:05:25s. Time for last 1,000,000: 2s. Last read position: chr4:94,234,095 INFO 2026-06-08 09:05:51 MarkDuplicates Tracking 1354468 as yet unmatched pairs. 25410 records in RAM. INFO 2026-06-08 09:05:53 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:05:27s. Time for last 1,000,000: 2s. Last read position: chr4:105,241,300 INFO 2026-06-08 09:05:53 MarkDuplicates Tracking 1352129 as yet unmatched pairs. 22922 records in RAM. INFO 2026-06-08 09:05:55 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:05:29s. Time for last 1,000,000: 2s. Last read position: chr4:112,457,620 INFO 2026-06-08 09:05:55 MarkDuplicates Tracking 1349529 as yet unmatched pairs. 20182 records in RAM. INFO 2026-06-08 09:05:57 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:05:31s. Time for last 1,000,000: 1s. Last read position: chr4:122,240,273 INFO 2026-06-08 09:05:57 MarkDuplicates Tracking 1347864 as yet unmatched pairs. 18430 records in RAM. INFO 2026-06-08 09:05:59 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:05:33s. Time for last 1,000,000: 2s. Last read position: chr4:128,287,430 INFO 2026-06-08 09:05:59 MarkDuplicates Tracking 1344737 as yet unmatched pairs. 15213 records in RAM. INFO 2026-06-08 09:06:01 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:05:35s. Time for last 1,000,000: 1s. Last read position: chr4:142,028,777 INFO 2026-06-08 09:06:01 MarkDuplicates Tracking 1342254 as yet unmatched pairs. 12632 records in RAM. INFO 2026-06-08 09:06:03 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:05:37s. Time for last 1,000,000: 2s. Last read position: chr4:151,099,697 INFO 2026-06-08 09:06:03 MarkDuplicates Tracking 1340505 as yet unmatched pairs. 10785 records in RAM. INFO 2026-06-08 09:06:05 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:05:39s. Time for last 1,000,000: 1s. Last read position: chr4:158,868,751 INFO 2026-06-08 09:06:05 MarkDuplicates Tracking 1337194 as yet unmatched pairs. 7392 records in RAM. INFO 2026-06-08 09:06:07 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:05:41s. Time for last 1,000,000: 2s. Last read position: chr4:182,792,969 INFO 2026-06-08 09:06:07 MarkDuplicates Tracking 1334697 as yet unmatched pairs. 4739 records in RAM. INFO 2026-06-08 09:06:09 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:05:43s. Time for last 1,000,000: 2s. Last read position: chr4:186,619,575 INFO 2026-06-08 09:06:09 MarkDuplicates Tracking 1332724 as yet unmatched pairs. 2694 records in RAM. INFO 2026-06-08 09:06:12 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:05:46s. Time for last 1,000,000: 3s. Last read position: chr5:993,209 INFO 2026-06-08 09:06:12 MarkDuplicates Tracking 1329281 as yet unmatched pairs. 101152 records in RAM. INFO 2026-06-08 09:06:14 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:05:48s. Time for last 1,000,000: 2s. Last read position: chr5:14,290,727 INFO 2026-06-08 09:06:14 MarkDuplicates Tracking 1326772 as yet unmatched pairs. 98551 records in RAM. INFO 2026-06-08 09:06:17 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:05:51s. Time for last 1,000,000: 2s. Last read position: chr5:14,487,903 INFO 2026-06-08 09:06:17 MarkDuplicates Tracking 1323570 as yet unmatched pairs. 95303 records in RAM. INFO 2026-06-08 09:06:19 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:05:53s. Time for last 1,000,000: 2s. Last read position: chr5:32,403,132 INFO 2026-06-08 09:06:19 MarkDuplicates Tracking 1320665 as yet unmatched pairs. 92308 records in RAM. INFO 2026-06-08 09:06:20 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:05:54s. Time for last 1,000,000: 1s. Last read position: chr5:37,230,685 INFO 2026-06-08 09:06:20 MarkDuplicates Tracking 1318229 as yet unmatched pairs. 89769 records in RAM. INFO 2026-06-08 09:06:22 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:05:56s. Time for last 1,000,000: 2s. Last read position: chr5:52,939,587 INFO 2026-06-08 09:06:22 MarkDuplicates Tracking 1315845 as yet unmatched pairs. 87319 records in RAM. INFO 2026-06-08 09:06:25 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:05:59s. Time for last 1,000,000: 2s. Last read position: chr5:65,795,420 INFO 2026-06-08 09:06:25 MarkDuplicates Tracking 1313097 as yet unmatched pairs. 84450 records in RAM. INFO 2026-06-08 09:06:26 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:06:00s. Time for last 1,000,000: 1s. Last read position: chr5:70,101,398 INFO 2026-06-08 09:06:26 MarkDuplicates Tracking 1311145 as yet unmatched pairs. 82410 records in RAM. INFO 2026-06-08 09:06:28 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:06:02s. Time for last 1,000,000: 1s. Last read position: chr5:72,199,866 INFO 2026-06-08 09:06:28 MarkDuplicates Tracking 1309529 as yet unmatched pairs. 80738 records in RAM. INFO 2026-06-08 09:06:30 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:06:04s. Time for last 1,000,000: 1s. Last read position: chr5:77,693,291 INFO 2026-06-08 09:06:30 MarkDuplicates Tracking 1307394 as yet unmatched pairs. 78539 records in RAM. INFO 2026-06-08 09:06:32 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:06:06s. Time for last 1,000,000: 2s. Last read position: chr5:81,473,707 INFO 2026-06-08 09:06:32 MarkDuplicates Tracking 1305103 as yet unmatched pairs. 76125 records in RAM. INFO 2026-06-08 09:06:34 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:06:08s. Time for last 1,000,000: 2s. Last read position: chr5:83,545,612 INFO 2026-06-08 09:06:34 MarkDuplicates Tracking 1302645 as yet unmatched pairs. 73599 records in RAM. INFO 2026-06-08 09:06:36 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:06:10s. Time for last 1,000,000: 1s. Last read position: chr5:98,901,224 INFO 2026-06-08 09:06:36 MarkDuplicates Tracking 1299850 as yet unmatched pairs. 70651 records in RAM. INFO 2026-06-08 09:06:38 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:06:12s. Time for last 1,000,000: 2s. Last read position: chr5:116,446,923 INFO 2026-06-08 09:06:38 MarkDuplicates Tracking 1297512 as yet unmatched pairs. 68190 records in RAM. INFO 2026-06-08 09:06:40 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:06:14s. Time for last 1,000,000: 1s. Last read position: chr5:128,280,192 INFO 2026-06-08 09:06:40 MarkDuplicates Tracking 1294737 as yet unmatched pairs. 65340 records in RAM. INFO 2026-06-08 09:06:42 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:06:16s. Time for last 1,000,000: 2s. Last read position: chr5:132,934,357 INFO 2026-06-08 09:06:42 MarkDuplicates Tracking 1292403 as yet unmatched pairs. 62951 records in RAM. INFO 2026-06-08 09:06:44 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:06:18s. Time for last 1,000,000: 2s. Last read position: chr5:136,160,965 INFO 2026-06-08 09:06:44 MarkDuplicates Tracking 1289371 as yet unmatched pairs. 59873 records in RAM. INFO 2026-06-08 09:06:46 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:06:20s. Time for last 1,000,000: 1s. Last read position: chr5:138,466,990 INFO 2026-06-08 09:06:46 MarkDuplicates Tracking 1287430 as yet unmatched pairs. 57898 records in RAM. INFO 2026-06-08 09:06:48 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:06:22s. Time for last 1,000,000: 1s. Last read position: chr5:138,467,837 INFO 2026-06-08 09:06:48 MarkDuplicates Tracking 1285020 as yet unmatched pairs. 55462 records in RAM. INFO 2026-06-08 09:06:50 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:06:24s. Time for last 1,000,000: 2s. Last read position: chr5:139,481,436 INFO 2026-06-08 09:06:50 MarkDuplicates Tracking 1280967 as yet unmatched pairs. 51353 records in RAM. INFO 2026-06-08 09:06:52 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:06:26s. Time for last 1,000,000: 1s. Last read position: chr5:140,834,824 INFO 2026-06-08 09:06:52 MarkDuplicates Tracking 1278190 as yet unmatched pairs. 48351 records in RAM. INFO 2026-06-08 09:06:54 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:06:28s. Time for last 1,000,000: 1s. Last read position: chr5:141,101,992 INFO 2026-06-08 09:06:54 MarkDuplicates Tracking 1276520 as yet unmatched pairs. 46648 records in RAM. INFO 2026-06-08 09:06:56 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:06:30s. Time for last 1,000,000: 1s. Last read position: chr5:141,179,381 INFO 2026-06-08 09:06:56 MarkDuplicates Tracking 1273716 as yet unmatched pairs. 43831 records in RAM. INFO 2026-06-08 09:06:57 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:06:31s. Time for last 1,000,000: 1s. Last read position: chr5:141,194,036 INFO 2026-06-08 09:06:57 MarkDuplicates Tracking 1271295 as yet unmatched pairs. 41378 records in RAM. INFO 2026-06-08 09:06:59 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:06:33s. Time for last 1,000,000: 1s. Last read position: chr5:141,235,702 INFO 2026-06-08 09:06:59 MarkDuplicates Tracking 1269044 as yet unmatched pairs. 39101 records in RAM. INFO 2026-06-08 09:07:01 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:06:35s. Time for last 1,000,000: 1s. Last read position: chr5:141,477,097 INFO 2026-06-08 09:07:01 MarkDuplicates Tracking 1266570 as yet unmatched pairs. 36564 records in RAM. INFO 2026-06-08 09:07:03 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:06:37s. Time for last 1,000,000: 2s. Last read position: chr5:142,314,997 INFO 2026-06-08 09:07:03 MarkDuplicates Tracking 1264693 as yet unmatched pairs. 34628 records in RAM. INFO 2026-06-08 09:07:05 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:06:39s. Time for last 1,000,000: 2s. Last read position: chr5:148,086,489 INFO 2026-06-08 09:07:05 MarkDuplicates Tracking 1260816 as yet unmatched pairs. 30638 records in RAM. INFO 2026-06-08 09:07:07 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:06:41s. Time for last 1,000,000: 2s. Last read position: chr5:150,131,968 INFO 2026-06-08 09:07:07 MarkDuplicates Tracking 1258354 as yet unmatched pairs. 28125 records in RAM. INFO 2026-06-08 09:07:09 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:06:43s. Time for last 1,000,000: 2s. Last read position: chr5:150,648,780 INFO 2026-06-08 09:07:09 MarkDuplicates Tracking 1255259 as yet unmatched pairs. 24986 records in RAM. INFO 2026-06-08 09:07:11 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:06:45s. Time for last 1,000,000: 1s. Last read position: chr5:151,803,934 INFO 2026-06-08 09:07:11 MarkDuplicates Tracking 1252251 as yet unmatched pairs. 21927 records in RAM. INFO 2026-06-08 09:07:13 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:06:47s. Time for last 1,000,000: 2s. Last read position: chr5:159,268,896 INFO 2026-06-08 09:07:13 MarkDuplicates Tracking 1249511 as yet unmatched pairs. 19069 records in RAM. INFO 2026-06-08 09:07:15 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:06:49s. Time for last 1,000,000: 2s. Last read position: chr5:168,823,295 INFO 2026-06-08 09:07:15 MarkDuplicates Tracking 1247526 as yet unmatched pairs. 17013 records in RAM. INFO 2026-06-08 09:07:17 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:06:51s. Time for last 1,000,000: 1s. Last read position: chr5:171,392,748 INFO 2026-06-08 09:07:17 MarkDuplicates Tracking 1248467 as yet unmatched pairs. 17812 records in RAM. INFO 2026-06-08 09:07:19 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:06:53s. Time for last 1,000,000: 2s. Last read position: chr5:173,613,240 INFO 2026-06-08 09:07:19 MarkDuplicates Tracking 1242203 as yet unmatched pairs. 11515 records in RAM. INFO 2026-06-08 09:07:21 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:06:55s. Time for last 1,000,000: 1s. Last read position: chr5:177,460,604 INFO 2026-06-08 09:07:21 MarkDuplicates Tracking 1239457 as yet unmatched pairs. 8732 records in RAM. INFO 2026-06-08 09:07:23 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:06:57s. Time for last 1,000,000: 1s. Last read position: chr5:179,614,887 INFO 2026-06-08 09:07:23 MarkDuplicates Tracking 1236608 as yet unmatched pairs. 5819 records in RAM. INFO 2026-06-08 09:07:25 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:06:59s. Time for last 1,000,000: 1s. Last read position: chr5:179,833,711 INFO 2026-06-08 09:07:25 MarkDuplicates Tracking 1233694 as yet unmatched pairs. 2868 records in RAM. INFO 2026-06-08 09:07:27 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:07:01s. Time for last 1,000,000: 2s. Last read position: chr6:599,175 INFO 2026-06-08 09:07:27 MarkDuplicates Tracking 1230997 as yet unmatched pairs. 83916 records in RAM. INFO 2026-06-08 09:07:29 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:07:03s. Time for last 1,000,000: 1s. Last read position: chr6:7,414,340 INFO 2026-06-08 09:07:29 MarkDuplicates Tracking 1228011 as yet unmatched pairs. 80833 records in RAM. INFO 2026-06-08 09:07:32 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:07:06s. Time for last 1,000,000: 2s. Last read position: chr6:17,675,652 INFO 2026-06-08 09:07:32 MarkDuplicates Tracking 1225550 as yet unmatched pairs. 78254 records in RAM. INFO 2026-06-08 09:07:34 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:07:08s. Time for last 1,000,000: 2s. Last read position: chr6:25,983,606 INFO 2026-06-08 09:07:34 MarkDuplicates Tracking 1222157 as yet unmatched pairs. 74739 records in RAM. INFO 2026-06-08 09:07:36 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:07:10s. Time for last 1,000,000: 1s. Last read position: chr6:26,377,182 INFO 2026-06-08 09:07:36 MarkDuplicates Tracking 1218985 as yet unmatched pairs. 71542 records in RAM. INFO 2026-06-08 09:07:38 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:07:12s. Time for last 1,000,000: 1s. Last read position: chr6:30,068,596 INFO 2026-06-08 09:07:38 MarkDuplicates Tracking 1216382 as yet unmatched pairs. 68885 records in RAM. INFO 2026-06-08 09:07:40 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:07:14s. Time for last 1,000,000: 2s. Last read position: chr6:30,920,166 INFO 2026-06-08 09:07:40 MarkDuplicates Tracking 1213441 as yet unmatched pairs. 65906 records in RAM. INFO 2026-06-08 09:07:41 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:07:15s. Time for last 1,000,000: 1s. Last read position: chr6:31,646,410 INFO 2026-06-08 09:07:41 MarkDuplicates Tracking 1210646 as yet unmatched pairs. 63062 records in RAM. INFO 2026-06-08 09:07:43 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:07:17s. Time for last 1,000,000: 1s. Last read position: chr6:32,035,184 INFO 2026-06-08 09:07:43 MarkDuplicates Tracking 1207857 as yet unmatched pairs. 60237 records in RAM. INFO 2026-06-08 09:07:45 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:07:19s. Time for last 1,000,000: 2s. Last read position: chr6:33,201,249 INFO 2026-06-08 09:07:45 MarkDuplicates Tracking 1205252 as yet unmatched pairs. 57606 records in RAM. INFO 2026-06-08 09:07:47 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:07:21s. Time for last 1,000,000: 1s. Last read position: chr6:33,444,612 INFO 2026-06-08 09:07:47 MarkDuplicates Tracking 1202342 as yet unmatched pairs. 54655 records in RAM. INFO 2026-06-08 09:07:49 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:07:23s. Time for last 1,000,000: 2s. Last read position: chr6:36,601,169 INFO 2026-06-08 09:07:49 MarkDuplicates Tracking 1199424 as yet unmatched pairs. 51671 records in RAM. INFO 2026-06-08 09:07:51 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:07:25s. Time for last 1,000,000: 2s. Last read position: chr6:42,263,536 INFO 2026-06-08 09:07:51 MarkDuplicates Tracking 1196521 as yet unmatched pairs. 48678 records in RAM. INFO 2026-06-08 09:07:53 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:07:27s. Time for last 1,000,000: 1s. Last read position: chr6:43,340,217 INFO 2026-06-08 09:07:53 MarkDuplicates Tracking 1193570 as yet unmatched pairs. 45665 records in RAM. INFO 2026-06-08 09:07:55 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:07:29s. Time for last 1,000,000: 2s. Last read position: chr6:47,574,168 INFO 2026-06-08 09:07:55 MarkDuplicates Tracking 1190800 as yet unmatched pairs. 42835 records in RAM. INFO 2026-06-08 09:07:57 MarkDuplicates Read 217,000,000 records. Elapsed time: 00:07:31s. Time for last 1,000,000: 2s. Last read position: chr6:56,603,325 INFO 2026-06-08 09:07:57 MarkDuplicates Tracking 1189022 as yet unmatched pairs. 40974 records in RAM. INFO 2026-06-08 09:07:59 MarkDuplicates Read 218,000,000 records. Elapsed time: 00:07:33s. Time for last 1,000,000: 1s. Last read position: chr6:70,860,209 INFO 2026-06-08 09:07:59 MarkDuplicates Tracking 1186026 as yet unmatched pairs. 37903 records in RAM. INFO 2026-06-08 09:08:01 MarkDuplicates Read 219,000,000 records. Elapsed time: 00:07:35s. Time for last 1,000,000: 2s. Last read position: chr6:79,016,559 INFO 2026-06-08 09:08:01 MarkDuplicates Tracking 1183673 as yet unmatched pairs. 35484 records in RAM. INFO 2026-06-08 09:08:03 MarkDuplicates Read 220,000,000 records. Elapsed time: 00:07:37s. Time for last 1,000,000: 1s. Last read position: chr6:87,524,616 INFO 2026-06-08 09:08:03 MarkDuplicates Tracking 1181092 as yet unmatched pairs. 32803 records in RAM. INFO 2026-06-08 09:08:05 MarkDuplicates Read 221,000,000 records. Elapsed time: 00:07:39s. Time for last 1,000,000: 2s. Last read position: chr6:99,406,054 INFO 2026-06-08 09:08:05 MarkDuplicates Tracking 1178383 as yet unmatched pairs. 30032 records in RAM. INFO 2026-06-08 09:08:07 MarkDuplicates Read 222,000,000 records. Elapsed time: 00:07:41s. Time for last 1,000,000: 1s. Last read position: chr6:109,146,779 INFO 2026-06-08 09:08:07 MarkDuplicates Tracking 1175856 as yet unmatched pairs. 27434 records in RAM. INFO 2026-06-08 09:08:09 MarkDuplicates Read 223,000,000 records. Elapsed time: 00:07:43s. Time for last 1,000,000: 1s. Last read position: chr6:113,859,682 INFO 2026-06-08 09:08:09 MarkDuplicates Tracking 1173279 as yet unmatched pairs. 24761 records in RAM. INFO 2026-06-08 09:08:11 MarkDuplicates Read 224,000,000 records. Elapsed time: 00:07:45s. Time for last 1,000,000: 1s. Last read position: chr6:125,292,888 INFO 2026-06-08 09:08:11 MarkDuplicates Tracking 1170448 as yet unmatched pairs. 21857 records in RAM. INFO 2026-06-08 09:08:13 MarkDuplicates Read 225,000,000 records. Elapsed time: 00:07:47s. Time for last 1,000,000: 2s. Last read position: chr6:130,899,526 INFO 2026-06-08 09:08:13 MarkDuplicates Tracking 1167904 as yet unmatched pairs. 19216 records in RAM. INFO 2026-06-08 09:08:14 MarkDuplicates Read 226,000,000 records. Elapsed time: 00:07:48s. Time for last 1,000,000: 1s. Last read position: chr6:138,432,795 INFO 2026-06-08 09:08:14 MarkDuplicates Tracking 1165435 as yet unmatched pairs. 16680 records in RAM. INFO 2026-06-08 09:08:16 MarkDuplicates Read 227,000,000 records. Elapsed time: 00:07:50s. Time for last 1,000,000: 2s. Last read position: chr6:149,378,343 INFO 2026-06-08 09:08:16 MarkDuplicates Tracking 1162692 as yet unmatched pairs. 13816 records in RAM. INFO 2026-06-08 09:08:18 MarkDuplicates Read 228,000,000 records. Elapsed time: 00:07:52s. Time for last 1,000,000: 1s. Last read position: chr6:152,354,682 INFO 2026-06-08 09:08:18 MarkDuplicates Tracking 1160099 as yet unmatched pairs. 11164 records in RAM. INFO 2026-06-08 09:08:20 MarkDuplicates Read 229,000,000 records. Elapsed time: 00:07:54s. Time for last 1,000,000: 1s. Last read position: chr6:157,906,183 INFO 2026-06-08 09:08:20 MarkDuplicates Tracking 1157423 as yet unmatched pairs. 8409 records in RAM. INFO 2026-06-08 09:08:22 MarkDuplicates Read 230,000,000 records. Elapsed time: 00:07:56s. Time for last 1,000,000: 1s. Last read position: chr6:160,096,501 INFO 2026-06-08 09:08:22 MarkDuplicates Tracking 1154689 as yet unmatched pairs. 5611 records in RAM. INFO 2026-06-08 09:08:24 MarkDuplicates Read 231,000,000 records. Elapsed time: 00:07:58s. Time for last 1,000,000: 1s. Last read position: chr6:163,570,701 INFO 2026-06-08 09:08:24 MarkDuplicates Tracking 1153029 as yet unmatched pairs. 3903 records in RAM. INFO 2026-06-08 09:08:27 MarkDuplicates Read 232,000,000 records. Elapsed time: 00:08:01s. Time for last 1,000,000: 3s. Last read position: chr7:838,884 INFO 2026-06-08 09:08:27 MarkDuplicates Tracking 1149067 as yet unmatched pairs. 95333 records in RAM. INFO 2026-06-08 09:08:29 MarkDuplicates Read 233,000,000 records. Elapsed time: 00:08:03s. Time for last 1,000,000: 2s. Last read position: chr7:5,048,041 INFO 2026-06-08 09:08:29 MarkDuplicates Tracking 1145470 as yet unmatched pairs. 91691 records in RAM. INFO 2026-06-08 09:08:31 MarkDuplicates Read 234,000,000 records. Elapsed time: 00:08:05s. Time for last 1,000,000: 1s. Last read position: chr7:5,528,025 INFO 2026-06-08 09:08:31 MarkDuplicates Tracking 1147518 as yet unmatched pairs. 93706 records in RAM. INFO 2026-06-08 09:08:33 MarkDuplicates Read 235,000,000 records. Elapsed time: 00:08:07s. Time for last 1,000,000: 1s. Last read position: chr7:6,164,889 INFO 2026-06-08 09:08:33 MarkDuplicates Tracking 1139281 as yet unmatched pairs. 85425 records in RAM. INFO 2026-06-08 09:08:35 MarkDuplicates Read 236,000,000 records. Elapsed time: 00:08:09s. Time for last 1,000,000: 1s. Last read position: chr7:13,935,781 INFO 2026-06-08 09:08:35 MarkDuplicates Tracking 1136757 as yet unmatched pairs. 82837 records in RAM. INFO 2026-06-08 09:08:37 MarkDuplicates Read 237,000,000 records. Elapsed time: 00:08:11s. Time for last 1,000,000: 1s. Last read position: chr7:17,327,757 INFO 2026-06-08 09:08:37 MarkDuplicates Tracking 1133904 as yet unmatched pairs. 79753 records in RAM. INFO 2026-06-08 09:08:39 MarkDuplicates Read 238,000,000 records. Elapsed time: 00:08:13s. Time for last 1,000,000: 2s. Last read position: chr7:27,108,172 INFO 2026-06-08 09:08:39 MarkDuplicates Tracking 1131455 as yet unmatched pairs. 77246 records in RAM. INFO 2026-06-08 09:08:40 MarkDuplicates Read 239,000,000 records. Elapsed time: 00:08:14s. Time for last 1,000,000: 1s. Last read position: chr7:35,898,280 INFO 2026-06-08 09:08:40 MarkDuplicates Tracking 1128616 as yet unmatched pairs. 74345 records in RAM. INFO 2026-06-08 09:08:43 MarkDuplicates Read 240,000,000 records. Elapsed time: 00:08:17s. Time for last 1,000,000: 2s. Last read position: chr7:44,106,772 INFO 2026-06-08 09:08:43 MarkDuplicates Tracking 1125876 as yet unmatched pairs. 71508 records in RAM. INFO 2026-06-08 09:08:45 MarkDuplicates Read 241,000,000 records. Elapsed time: 00:08:19s. Time for last 1,000,000: 1s. Last read position: chr7:55,019,172 INFO 2026-06-08 09:08:45 MarkDuplicates Tracking 1123108 as yet unmatched pairs. 68689 records in RAM. INFO 2026-06-08 09:08:47 MarkDuplicates Read 242,000,000 records. Elapsed time: 00:08:21s. Time for last 1,000,000: 2s. Last read position: chr7:55,198,732 INFO 2026-06-08 09:08:47 MarkDuplicates Tracking 1122133 as yet unmatched pairs. 67672 records in RAM. INFO 2026-06-08 09:08:49 MarkDuplicates Read 243,000,000 records. Elapsed time: 00:08:23s. Time for last 1,000,000: 2s. Last read position: chr7:64,834,146 INFO 2026-06-08 09:08:49 MarkDuplicates Tracking 1117327 as yet unmatched pairs. 62838 records in RAM. INFO 2026-06-08 09:08:51 MarkDuplicates Read 244,000,000 records. Elapsed time: 00:08:25s. Time for last 1,000,000: 1s. Last read position: chr7:72,942,220 INFO 2026-06-08 09:08:51 MarkDuplicates Tracking 1115863 as yet unmatched pairs. 61263 records in RAM. INFO 2026-06-08 09:08:52 MarkDuplicates Read 245,000,000 records. Elapsed time: 00:08:26s. Time for last 1,000,000: 1s. Last read position: chr7:73,477,083 INFO 2026-06-08 09:08:52 MarkDuplicates Tracking 1114450 as yet unmatched pairs. 59842 records in RAM. INFO 2026-06-08 09:08:54 MarkDuplicates Read 246,000,000 records. Elapsed time: 00:08:28s. Time for last 1,000,000: 1s. Last read position: chr7:75,199,713 INFO 2026-06-08 09:08:54 MarkDuplicates Tracking 1112292 as yet unmatched pairs. 57645 records in RAM. INFO 2026-06-08 09:08:56 MarkDuplicates Read 247,000,000 records. Elapsed time: 00:08:30s. Time for last 1,000,000: 1s. Last read position: chr7:76,048,214 INFO 2026-06-08 09:08:56 MarkDuplicates Tracking 1109919 as yet unmatched pairs. 55257 records in RAM. INFO 2026-06-08 09:08:58 MarkDuplicates Read 248,000,000 records. Elapsed time: 00:08:32s. Time for last 1,000,000: 1s. Last read position: chr7:81,769,910 INFO 2026-06-08 09:08:58 MarkDuplicates Tracking 1107647 as yet unmatched pairs. 52928 records in RAM. INFO 2026-06-08 09:09:00 MarkDuplicates Read 249,000,000 records. Elapsed time: 00:08:34s. Time for last 1,000,000: 1s. Last read position: chr7:92,070,030 INFO 2026-06-08 09:09:00 MarkDuplicates Tracking 1105737 as yet unmatched pairs. 50962 records in RAM. INFO 2026-06-08 09:09:02 MarkDuplicates Read 250,000,000 records. Elapsed time: 00:08:36s. Time for last 1,000,000: 2s. Last read position: chr7:94,404,874 INFO 2026-06-08 09:09:02 MarkDuplicates Tracking 1104532 as yet unmatched pairs. 49711 records in RAM. INFO 2026-06-08 09:09:04 MarkDuplicates Read 251,000,000 records. Elapsed time: 00:08:38s. Time for last 1,000,000: 2s. Last read position: chr7:94,425,757 INFO 2026-06-08 09:09:04 MarkDuplicates Tracking 1100578 as yet unmatched pairs. 45704 records in RAM. INFO 2026-06-08 09:09:06 MarkDuplicates Read 252,000,000 records. Elapsed time: 00:08:40s. Time for last 1,000,000: 2s. Last read position: chr7:98,912,049 INFO 2026-06-08 09:09:06 MarkDuplicates Tracking 1096830 as yet unmatched pairs. 41906 records in RAM. INFO 2026-06-08 09:09:08 MarkDuplicates Read 253,000,000 records. Elapsed time: 00:08:42s. Time for last 1,000,000: 2s. Last read position: chr7:100,090,463 INFO 2026-06-08 09:09:08 MarkDuplicates Tracking 1093931 as yet unmatched pairs. 38964 records in RAM. INFO 2026-06-08 09:09:10 MarkDuplicates Read 254,000,000 records. Elapsed time: 00:08:44s. Time for last 1,000,000: 1s. Last read position: chr7:100,678,692 INFO 2026-06-08 09:09:10 MarkDuplicates Tracking 1091108 as yet unmatched pairs. 36108 records in RAM. INFO 2026-06-08 09:09:12 MarkDuplicates Read 255,000,000 records. Elapsed time: 00:08:46s. Time for last 1,000,000: 1s. Last read position: chr7:102,355,954 INFO 2026-06-08 09:09:12 MarkDuplicates Tracking 1088254 as yet unmatched pairs. 33221 records in RAM. INFO 2026-06-08 09:09:14 MarkDuplicates Read 256,000,000 records. Elapsed time: 00:08:48s. Time for last 1,000,000: 1s. Last read position: chr7:103,341,854 INFO 2026-06-08 09:09:14 MarkDuplicates Tracking 1086809 as yet unmatched pairs. 31756 records in RAM. INFO 2026-06-08 09:09:15 MarkDuplicates Read 257,000,000 records. Elapsed time: 00:08:49s. Time for last 1,000,000: 1s. Last read position: chr7:107,926,315 INFO 2026-06-08 09:09:15 MarkDuplicates Tracking 1086932 as yet unmatched pairs. 31816 records in RAM. INFO 2026-06-08 09:09:17 MarkDuplicates Read 258,000,000 records. Elapsed time: 00:08:51s. Time for last 1,000,000: 2s. Last read position: chr7:107,953,738 INFO 2026-06-08 09:09:17 MarkDuplicates Tracking 1083026 as yet unmatched pairs. 27865 records in RAM. INFO 2026-06-08 09:09:19 MarkDuplicates Read 259,000,000 records. Elapsed time: 00:08:53s. Time for last 1,000,000: 1s. Last read position: chr7:111,760,217 INFO 2026-06-08 09:09:19 MarkDuplicates Tracking 1079258 as yet unmatched pairs. 24045 records in RAM. INFO 2026-06-08 09:09:21 MarkDuplicates Read 260,000,000 records. Elapsed time: 00:08:55s. Time for last 1,000,000: 2s. Last read position: chr7:127,707,599 INFO 2026-06-08 09:09:21 MarkDuplicates Tracking 1078303 as yet unmatched pairs. 22999 records in RAM. INFO 2026-06-08 09:09:23 MarkDuplicates Read 261,000,000 records. Elapsed time: 00:08:57s. Time for last 1,000,000: 2s. Last read position: chr7:129,211,652 INFO 2026-06-08 09:09:23 MarkDuplicates Tracking 1073910 as yet unmatched pairs. 18558 records in RAM. INFO 2026-06-08 09:09:26 MarkDuplicates Read 262,000,000 records. Elapsed time: 00:09:00s. Time for last 1,000,000: 2s. Last read position: chr7:134,933,235 INFO 2026-06-08 09:09:26 MarkDuplicates Tracking 1071582 as yet unmatched pairs. 16149 records in RAM. INFO 2026-06-08 09:09:28 MarkDuplicates Read 263,000,000 records. Elapsed time: 00:09:02s. Time for last 1,000,000: 2s. Last read position: chr7:138,584,814 INFO 2026-06-08 09:09:28 MarkDuplicates Tracking 1068787 as yet unmatched pairs. 13307 records in RAM. INFO 2026-06-08 09:09:29 MarkDuplicates Read 264,000,000 records. Elapsed time: 00:09:03s. Time for last 1,000,000: 1s. Last read position: chr7:140,739,812 INFO 2026-06-08 09:09:29 MarkDuplicates Tracking 1066057 as yet unmatched pairs. 10530 records in RAM. INFO 2026-06-08 09:09:31 MarkDuplicates Read 265,000,000 records. Elapsed time: 00:09:05s. Time for last 1,000,000: 2s. Last read position: chr7:149,008,279 INFO 2026-06-08 09:09:31 MarkDuplicates Tracking 1063259 as yet unmatched pairs. 7673 records in RAM. INFO 2026-06-08 09:09:33 MarkDuplicates Read 266,000,000 records. Elapsed time: 00:09:07s. Time for last 1,000,000: 2s. Last read position: chr7:151,242,161 INFO 2026-06-08 09:09:33 MarkDuplicates Tracking 1059964 as yet unmatched pairs. 4334 records in RAM. INFO 2026-06-08 09:09:35 MarkDuplicates Read 267,000,000 records. Elapsed time: 00:09:09s. Time for last 1,000,000: 1s. Last read position: chr7:155,737,618 INFO 2026-06-08 09:09:35 MarkDuplicates Tracking 1057194 as yet unmatched pairs. 1478 records in RAM. INFO 2026-06-08 09:09:38 MarkDuplicates Read 268,000,000 records. Elapsed time: 00:09:12s. Time for last 1,000,000: 2s. Last read position: chr8:8,377,683 INFO 2026-06-08 09:09:38 MarkDuplicates Tracking 1054661 as yet unmatched pairs. 63928 records in RAM. INFO 2026-06-08 09:09:40 MarkDuplicates Read 269,000,000 records. Elapsed time: 00:09:14s. Time for last 1,000,000: 2s. Last read position: chr8:17,953,027 INFO 2026-06-08 09:09:40 MarkDuplicates Tracking 1052291 as yet unmatched pairs. 61447 records in RAM. INFO 2026-06-08 09:09:42 MarkDuplicates Read 270,000,000 records. Elapsed time: 00:09:16s. Time for last 1,000,000: 1s. Last read position: chr8:22,606,140 INFO 2026-06-08 09:09:42 MarkDuplicates Tracking 1049359 as yet unmatched pairs. 58453 records in RAM. INFO 2026-06-08 09:09:44 MarkDuplicates Read 271,000,000 records. Elapsed time: 00:09:18s. Time for last 1,000,000: 2s. Last read position: chr8:22,691,101 INFO 2026-06-08 09:09:44 MarkDuplicates Tracking 1046419 as yet unmatched pairs. 55486 records in RAM. INFO 2026-06-08 09:09:45 MarkDuplicates Read 272,000,000 records. Elapsed time: 00:09:19s. Time for last 1,000,000: 1s. Last read position: chr8:25,972,463 INFO 2026-06-08 09:09:45 MarkDuplicates Tracking 1043593 as yet unmatched pairs. 52620 records in RAM. INFO 2026-06-08 09:09:47 MarkDuplicates Read 273,000,000 records. Elapsed time: 00:09:21s. Time for last 1,000,000: 2s. Last read position: chr8:30,812,293 INFO 2026-06-08 09:09:47 MarkDuplicates Tracking 1040579 as yet unmatched pairs. 49527 records in RAM. INFO 2026-06-08 09:09:50 MarkDuplicates Read 274,000,000 records. Elapsed time: 00:09:24s. Time for last 1,000,000: 2s. Last read position: chr8:38,305,414 INFO 2026-06-08 09:09:50 MarkDuplicates Tracking 1037794 as yet unmatched pairs. 46685 records in RAM. INFO 2026-06-08 09:09:51 MarkDuplicates Read 275,000,000 records. Elapsed time: 00:09:25s. Time for last 1,000,000: 1s. Last read position: chr8:38,414,582 INFO 2026-06-08 09:09:51 MarkDuplicates Tracking 1035469 as yet unmatched pairs. 44328 records in RAM. INFO 2026-06-08 09:09:53 MarkDuplicates Read 276,000,000 records. Elapsed time: 00:09:27s. Time for last 1,000,000: 2s. Last read position: chr8:38,428,355 INFO 2026-06-08 09:09:53 MarkDuplicates Tracking 1037292 as yet unmatched pairs. 46117 records in RAM. INFO 2026-06-08 09:09:55 MarkDuplicates Read 277,000,000 records. Elapsed time: 00:09:29s. Time for last 1,000,000: 2s. Last read position: chr8:41,955,295 INFO 2026-06-08 09:09:55 MarkDuplicates Tracking 1029158 as yet unmatched pairs. 37943 records in RAM. INFO 2026-06-08 09:09:57 MarkDuplicates Read 278,000,000 records. Elapsed time: 00:09:31s. Time for last 1,000,000: 1s. Last read position: chr8:48,918,828 INFO 2026-06-08 09:09:57 MarkDuplicates Tracking 1026544 as yet unmatched pairs. 35277 records in RAM. INFO 2026-06-08 09:10:00 MarkDuplicates Read 279,000,000 records. Elapsed time: 00:09:34s. Time for last 1,000,000: 2s. Last read position: chr8:63,186,872 INFO 2026-06-08 09:10:00 MarkDuplicates Tracking 1023673 as yet unmatched pairs. 32356 records in RAM. INFO 2026-06-08 09:10:01 MarkDuplicates Read 280,000,000 records. Elapsed time: 00:09:35s. Time for last 1,000,000: 1s. Last read position: chr8:73,257,075 INFO 2026-06-08 09:10:01 MarkDuplicates Tracking 1021013 as yet unmatched pairs. 29616 records in RAM. INFO 2026-06-08 09:10:03 MarkDuplicates Read 281,000,000 records. Elapsed time: 00:09:37s. Time for last 1,000,000: 1s. Last read position: chr8:86,480,315 INFO 2026-06-08 09:10:03 MarkDuplicates Tracking 1018818 as yet unmatched pairs. 27403 records in RAM. INFO 2026-06-08 09:10:05 MarkDuplicates Read 282,000,000 records. Elapsed time: 00:09:39s. Time for last 1,000,000: 2s. Last read position: chr8:97,713,685 INFO 2026-06-08 09:10:05 MarkDuplicates Tracking 1016361 as yet unmatched pairs. 24851 records in RAM. INFO 2026-06-08 09:10:07 MarkDuplicates Read 283,000,000 records. Elapsed time: 00:09:41s. Time for last 1,000,000: 1s. Last read position: chr8:100,709,518 INFO 2026-06-08 09:10:07 MarkDuplicates Tracking 1014188 as yet unmatched pairs. 22634 records in RAM. INFO 2026-06-08 09:10:09 MarkDuplicates Read 284,000,000 records. Elapsed time: 00:09:43s. Time for last 1,000,000: 2s. Last read position: chr8:108,203,463 INFO 2026-06-08 09:10:09 MarkDuplicates Tracking 1011172 as yet unmatched pairs. 19547 records in RAM. INFO 2026-06-08 09:10:11 MarkDuplicates Read 285,000,000 records. Elapsed time: 00:09:45s. Time for last 1,000,000: 2s. Last read position: chr8:124,487,496 INFO 2026-06-08 09:10:11 MarkDuplicates Tracking 1008350 as yet unmatched pairs. 16640 records in RAM. INFO 2026-06-08 09:10:13 MarkDuplicates Read 286,000,000 records. Elapsed time: 00:09:47s. Time for last 1,000,000: 1s. Last read position: chr8:133,213,089 INFO 2026-06-08 09:10:13 MarkDuplicates Tracking 1005591 as yet unmatched pairs. 13810 records in RAM. INFO 2026-06-08 09:10:15 MarkDuplicates Read 287,000,000 records. Elapsed time: 00:09:49s. Time for last 1,000,000: 2s. Last read position: chr8:143,605,830 INFO 2026-06-08 09:10:15 MarkDuplicates Tracking 1002535 as yet unmatched pairs. 10673 records in RAM. INFO 2026-06-08 09:10:17 MarkDuplicates Read 288,000,000 records. Elapsed time: 00:09:51s. Time for last 1,000,000: 1s. Last read position: chr8:143,922,651 INFO 2026-06-08 09:10:17 MarkDuplicates Tracking 999132 as yet unmatched pairs. 7234 records in RAM. INFO 2026-06-08 09:10:19 MarkDuplicates Read 289,000,000 records. Elapsed time: 00:09:53s. Time for last 1,000,000: 2s. Last read position: chr8:144,312,070 INFO 2026-06-08 09:10:19 MarkDuplicates Tracking 994842 as yet unmatched pairs. 2892 records in RAM. INFO 2026-06-08 09:10:22 MarkDuplicates Read 290,000,000 records. Elapsed time: 00:09:56s. Time for last 1,000,000: 2s. Last read position: chr9:713,068 INFO 2026-06-08 09:10:22 MarkDuplicates Tracking 991673 as yet unmatched pairs. 69086 records in RAM. INFO 2026-06-08 09:10:23 MarkDuplicates Read 291,000,000 records. Elapsed time: 00:09:57s. Time for last 1,000,000: 1s. Last read position: chr9:13,176,286 INFO 2026-06-08 09:10:23 MarkDuplicates Tracking 989218 as yet unmatched pairs. 66551 records in RAM. INFO 2026-06-08 09:10:26 MarkDuplicates Read 292,000,000 records. Elapsed time: 00:10:00s. Time for last 1,000,000: 2s. Last read position: chr9:14,307,187 INFO 2026-06-08 09:10:26 MarkDuplicates Tracking 987740 as yet unmatched pairs. 65040 records in RAM. INFO 2026-06-08 09:10:28 MarkDuplicates Read 293,000,000 records. Elapsed time: 00:10:02s. Time for last 1,000,000: 2s. Last read position: chr9:17,260,497 INFO 2026-06-08 09:10:28 MarkDuplicates Tracking 984231 as yet unmatched pairs. 61445 records in RAM. INFO 2026-06-08 09:10:29 MarkDuplicates Read 294,000,000 records. Elapsed time: 00:10:03s. Time for last 1,000,000: 1s. Last read position: chr9:33,468,961 INFO 2026-06-08 09:10:29 MarkDuplicates Tracking 981653 as yet unmatched pairs. 58838 records in RAM. INFO 2026-06-08 09:10:31 MarkDuplicates Read 295,000,000 records. Elapsed time: 00:10:05s. Time for last 1,000,000: 2s. Last read position: chr9:35,706,241 INFO 2026-06-08 09:10:31 MarkDuplicates Tracking 978802 as yet unmatched pairs. 55942 records in RAM. INFO 2026-06-08 09:10:33 MarkDuplicates Read 296,000,000 records. Elapsed time: 00:10:07s. Time for last 1,000,000: 1s. Last read position: chr9:40,482,484 INFO 2026-06-08 09:10:33 MarkDuplicates Tracking 976431 as yet unmatched pairs. 53462 records in RAM. INFO 2026-06-08 09:10:35 MarkDuplicates Read 297,000,000 records. Elapsed time: 00:10:09s. Time for last 1,000,000: 1s. Last read position: chr9:65,145,850 INFO 2026-06-08 09:10:35 MarkDuplicates Tracking 975523 as yet unmatched pairs. 52411 records in RAM. INFO 2026-06-08 09:10:37 MarkDuplicates Read 298,000,000 records. Elapsed time: 00:10:11s. Time for last 1,000,000: 1s. Last read position: chr9:79,707,136 INFO 2026-06-08 09:10:37 MarkDuplicates Tracking 973904 as yet unmatched pairs. 50719 records in RAM. INFO 2026-06-08 09:10:39 MarkDuplicates Read 299,000,000 records. Elapsed time: 00:10:13s. Time for last 1,000,000: 1s. Last read position: chr9:89,605,999 INFO 2026-06-08 09:10:39 MarkDuplicates Tracking 971233 as yet unmatched pairs. 47996 records in RAM. INFO 2026-06-08 09:10:41 MarkDuplicates Read 300,000,000 records. Elapsed time: 00:10:15s. Time for last 1,000,000: 2s. Last read position: chr9:93,660,228 INFO 2026-06-08 09:10:41 MarkDuplicates Tracking 968730 as yet unmatched pairs. 45419 records in RAM. INFO 2026-06-08 09:10:42 MarkDuplicates Read 301,000,000 records. Elapsed time: 00:10:16s. Time for last 1,000,000: 1s. Last read position: chr9:97,668,802 INFO 2026-06-08 09:10:42 MarkDuplicates Tracking 965897 as yet unmatched pairs. 42543 records in RAM. INFO 2026-06-08 09:10:45 MarkDuplicates Read 302,000,000 records. Elapsed time: 00:10:19s. Time for last 1,000,000: 2s. Last read position: chr9:105,520,134 INFO 2026-06-08 09:10:45 MarkDuplicates Tracking 962987 as yet unmatched pairs. 39560 records in RAM. INFO 2026-06-08 09:10:47 MarkDuplicates Read 303,000,000 records. Elapsed time: 00:10:21s. Time for last 1,000,000: 2s. Last read position: chr9:110,411,293 INFO 2026-06-08 09:10:47 MarkDuplicates Tracking 960543 as yet unmatched pairs. 37083 records in RAM. INFO 2026-06-08 09:10:48 MarkDuplicates Read 304,000,000 records. Elapsed time: 00:10:22s. Time for last 1,000,000: 1s. Last read position: chr9:114,237,022 INFO 2026-06-08 09:10:48 MarkDuplicates Tracking 957667 as yet unmatched pairs. 34137 records in RAM. INFO 2026-06-08 09:10:50 MarkDuplicates Read 305,000,000 records. Elapsed time: 00:10:24s. Time for last 1,000,000: 2s. Last read position: chr9:121,164,956 INFO 2026-06-08 09:10:50 MarkDuplicates Tracking 955173 as yet unmatched pairs. 31586 records in RAM. INFO 2026-06-08 09:10:52 MarkDuplicates Read 306,000,000 records. Elapsed time: 00:10:26s. Time for last 1,000,000: 1s. Last read position: chr9:124,804,255 INFO 2026-06-08 09:10:52 MarkDuplicates Tracking 951953 as yet unmatched pairs. 28334 records in RAM. INFO 2026-06-08 09:10:54 MarkDuplicates Read 307,000,000 records. Elapsed time: 00:10:28s. Time for last 1,000,000: 2s. Last read position: chr9:127,868,040 INFO 2026-06-08 09:10:54 MarkDuplicates Tracking 949036 as yet unmatched pairs. 25388 records in RAM. INFO 2026-06-08 09:10:56 MarkDuplicates Read 308,000,000 records. Elapsed time: 00:10:30s. Time for last 1,000,000: 2s. Last read position: chr9:128,584,740 INFO 2026-06-08 09:10:56 MarkDuplicates Tracking 945885 as yet unmatched pairs. 22208 records in RAM. INFO 2026-06-08 09:10:58 MarkDuplicates Read 309,000,000 records. Elapsed time: 00:10:32s. Time for last 1,000,000: 1s. Last read position: chr9:129,177,981 INFO 2026-06-08 09:10:58 MarkDuplicates Tracking 942749 as yet unmatched pairs. 19036 records in RAM. INFO 2026-06-08 09:11:00 MarkDuplicates Read 310,000,000 records. Elapsed time: 00:10:34s. Time for last 1,000,000: 2s. Last read position: chr9:130,885,173 INFO 2026-06-08 09:11:00 MarkDuplicates Tracking 940303 as yet unmatched pairs. 16555 records in RAM. INFO 2026-06-08 09:11:02 MarkDuplicates Read 311,000,000 records. Elapsed time: 00:10:36s. Time for last 1,000,000: 2s. Last read position: chr9:132,271,768 INFO 2026-06-08 09:11:02 MarkDuplicates Tracking 937155 as yet unmatched pairs. 13369 records in RAM. INFO 2026-06-08 09:11:04 MarkDuplicates Read 312,000,000 records. Elapsed time: 00:10:38s. Time for last 1,000,000: 1s. Last read position: chr9:133,730,103 INFO 2026-06-08 09:11:04 MarkDuplicates Tracking 934596 as yet unmatched pairs. 10769 records in RAM. INFO 2026-06-08 09:11:06 MarkDuplicates Read 313,000,000 records. Elapsed time: 00:10:40s. Time for last 1,000,000: 2s. Last read position: chr9:135,821,183 INFO 2026-06-08 09:11:06 MarkDuplicates Tracking 931459 as yet unmatched pairs. 7598 records in RAM. INFO 2026-06-08 09:11:08 MarkDuplicates Read 314,000,000 records. Elapsed time: 00:10:42s. Time for last 1,000,000: 1s. Last read position: chr9:136,523,074 INFO 2026-06-08 09:11:08 MarkDuplicates Tracking 928183 as yet unmatched pairs. 4291 records in RAM. INFO 2026-06-08 09:11:10 MarkDuplicates Read 315,000,000 records. Elapsed time: 00:10:44s. Time for last 1,000,000: 2s. Last read position: chr9:137,555,316 INFO 2026-06-08 09:11:10 MarkDuplicates Tracking 924731 as yet unmatched pairs. 807 records in RAM. INFO 2026-06-08 09:11:13 MarkDuplicates Read 316,000,000 records. Elapsed time: 00:10:47s. Time for last 1,000,000: 2s. Last read position: chr10:13,288,497 INFO 2026-06-08 09:11:13 MarkDuplicates Tracking 921952 as yet unmatched pairs. 31244 records in RAM. INFO 2026-06-08 09:11:14 MarkDuplicates Read 317,000,000 records. Elapsed time: 00:10:48s. Time for last 1,000,000: 1s. Last read position: chr10:24,597,560 INFO 2026-06-08 09:11:14 MarkDuplicates Tracking 919482 as yet unmatched pairs. 28703 records in RAM. INFO 2026-06-08 09:11:16 MarkDuplicates Read 318,000,000 records. Elapsed time: 00:10:50s. Time for last 1,000,000: 2s. Last read position: chr10:32,022,199 INFO 2026-06-08 09:11:16 MarkDuplicates Tracking 917238 as yet unmatched pairs. 26419 records in RAM. INFO 2026-06-08 09:11:18 MarkDuplicates Read 319,000,000 records. Elapsed time: 00:10:52s. Time for last 1,000,000: 1s. Last read position: chr10:45,699,148 INFO 2026-06-08 09:11:18 MarkDuplicates Tracking 914340 as yet unmatched pairs. 23470 records in RAM. INFO 2026-06-08 09:11:20 MarkDuplicates Read 320,000,000 records. Elapsed time: 00:10:54s. Time for last 1,000,000: 1s. Last read position: chr10:58,702,087 INFO 2026-06-08 09:11:20 MarkDuplicates Tracking 912841 as yet unmatched pairs. 21914 records in RAM. INFO 2026-06-08 09:11:22 MarkDuplicates Read 321,000,000 records. Elapsed time: 00:10:56s. Time for last 1,000,000: 1s. Last read position: chr10:63,215,406 INFO 2026-06-08 09:11:22 MarkDuplicates Tracking 910427 as yet unmatched pairs. 19475 records in RAM. INFO 2026-06-08 09:11:24 MarkDuplicates Read 322,000,000 records. Elapsed time: 00:10:58s. Time for last 1,000,000: 1s. Last read position: chr10:73,675,528 INFO 2026-06-08 09:11:24 MarkDuplicates Tracking 907514 as yet unmatched pairs. 16490 records in RAM. INFO 2026-06-08 09:11:26 MarkDuplicates Read 323,000,000 records. Elapsed time: 00:11:00s. Time for last 1,000,000: 1s. Last read position: chr10:84,371,770 INFO 2026-06-08 09:11:26 MarkDuplicates Tracking 905023 as yet unmatched pairs. 13958 records in RAM. INFO 2026-06-08 09:11:28 MarkDuplicates Read 324,000,000 records. Elapsed time: 00:11:02s. Time for last 1,000,000: 1s. Last read position: chr10:95,356,075 INFO 2026-06-08 09:11:28 MarkDuplicates Tracking 902625 as yet unmatched pairs. 11497 records in RAM. INFO 2026-06-08 09:11:30 MarkDuplicates Read 325,000,000 records. Elapsed time: 00:11:04s. Time for last 1,000,000: 2s. Last read position: chr10:101,803,768 INFO 2026-06-08 09:11:30 MarkDuplicates Tracking 900077 as yet unmatched pairs. 8910 records in RAM. INFO 2026-06-08 09:11:32 MarkDuplicates Read 326,000,000 records. Elapsed time: 00:11:06s. Time for last 1,000,000: 2s. Last read position: chr10:110,890,630 INFO 2026-06-08 09:11:32 MarkDuplicates Tracking 897260 as yet unmatched pairs. 6046 records in RAM. INFO 2026-06-08 09:11:33 MarkDuplicates Read 327,000,000 records. Elapsed time: 00:11:07s. Time for last 1,000,000: 1s. Last read position: chr10:119,670,073 INFO 2026-06-08 09:11:33 MarkDuplicates Tracking 894636 as yet unmatched pairs. 3343 records in RAM. INFO 2026-06-08 09:11:36 MarkDuplicates Read 328,000,000 records. Elapsed time: 00:11:10s. Time for last 1,000,000: 2s. Last read position: chr10:129,840,430 INFO 2026-06-08 09:11:36 MarkDuplicates Tracking 892134 as yet unmatched pairs. 777 records in RAM. INFO 2026-06-08 09:11:39 MarkDuplicates Read 329,000,000 records. Elapsed time: 00:11:13s. Time for last 1,000,000: 3s. Last read position: chr11:587,323 INFO 2026-06-08 09:11:39 MarkDuplicates Tracking 889148 as yet unmatched pairs. 100211 records in RAM. INFO 2026-06-08 09:11:41 MarkDuplicates Read 330,000,000 records. Elapsed time: 00:11:15s. Time for last 1,000,000: 1s. Last read position: chr11:2,132,956 INFO 2026-06-08 09:11:41 MarkDuplicates Tracking 886304 as yet unmatched pairs. 97293 records in RAM. INFO 2026-06-08 09:11:43 MarkDuplicates Read 331,000,000 records. Elapsed time: 00:11:17s. Time for last 1,000,000: 2s. Last read position: chr11:3,094,242 INFO 2026-06-08 09:11:43 MarkDuplicates Tracking 882479 as yet unmatched pairs. 93440 records in RAM. INFO 2026-06-08 09:11:45 MarkDuplicates Read 332,000,000 records. Elapsed time: 00:11:19s. Time for last 1,000,000: 1s. Last read position: chr11:6,622,331 INFO 2026-06-08 09:11:45 MarkDuplicates Tracking 879703 as yet unmatched pairs. 90631 records in RAM. INFO 2026-06-08 09:11:47 MarkDuplicates Read 333,000,000 records. Elapsed time: 00:11:21s. Time for last 1,000,000: 2s. Last read position: chr11:8,726,127 INFO 2026-06-08 09:11:47 MarkDuplicates Tracking 876702 as yet unmatched pairs. 87607 records in RAM. INFO 2026-06-08 09:11:49 MarkDuplicates Read 334,000,000 records. Elapsed time: 00:11:23s. Time for last 1,000,000: 2s. Last read position: chr11:10,804,913 INFO 2026-06-08 09:11:49 MarkDuplicates Tracking 874212 as yet unmatched pairs. 85060 records in RAM. INFO 2026-06-08 09:11:51 MarkDuplicates Read 335,000,000 records. Elapsed time: 00:11:25s. Time for last 1,000,000: 1s. Last read position: chr11:17,169,133 INFO 2026-06-08 09:11:51 MarkDuplicates Tracking 871276 as yet unmatched pairs. 82075 records in RAM. INFO 2026-06-08 09:11:53 MarkDuplicates Read 336,000,000 records. Elapsed time: 00:11:27s. Time for last 1,000,000: 2s. Last read position: chr11:32,976,362 INFO 2026-06-08 09:11:53 MarkDuplicates Tracking 868837 as yet unmatched pairs. 79595 records in RAM. INFO 2026-06-08 09:11:55 MarkDuplicates Read 337,000,000 records. Elapsed time: 00:11:29s. Time for last 1,000,000: 1s. Last read position: chr11:43,444,129 INFO 2026-06-08 09:11:55 MarkDuplicates Tracking 866064 as yet unmatched pairs. 76772 records in RAM. INFO 2026-06-08 09:11:57 MarkDuplicates Read 338,000,000 records. Elapsed time: 00:11:31s. Time for last 1,000,000: 2s. Last read position: chr11:46,376,322 INFO 2026-06-08 09:11:57 MarkDuplicates Tracking 862964 as yet unmatched pairs. 73641 records in RAM. INFO 2026-06-08 09:11:59 MarkDuplicates Read 339,000,000 records. Elapsed time: 00:11:33s. Time for last 1,000,000: 2s. Last read position: chr11:47,723,291 INFO 2026-06-08 09:11:59 MarkDuplicates Tracking 860342 as yet unmatched pairs. 70996 records in RAM. INFO 2026-06-08 09:12:00 MarkDuplicates Read 340,000,000 records. Elapsed time: 00:11:34s. Time for last 1,000,000: 1s. Last read position: chr11:57,811,460 INFO 2026-06-08 09:12:00 MarkDuplicates Tracking 858222 as yet unmatched pairs. 68852 records in RAM. INFO 2026-06-08 09:12:02 MarkDuplicates Read 341,000,000 records. Elapsed time: 00:11:36s. Time for last 1,000,000: 2s. Last read position: chr11:61,421,434 INFO 2026-06-08 09:12:02 MarkDuplicates Tracking 854495 as yet unmatched pairs. 65081 records in RAM. INFO 2026-06-08 09:12:04 MarkDuplicates Read 342,000,000 records. Elapsed time: 00:11:38s. Time for last 1,000,000: 1s. Last read position: chr11:62,528,698 INFO 2026-06-08 09:12:04 MarkDuplicates Tracking 852138 as yet unmatched pairs. 62697 records in RAM. INFO 2026-06-08 09:12:06 MarkDuplicates Read 343,000,000 records. Elapsed time: 00:11:40s. Time for last 1,000,000: 2s. Last read position: chr11:62,677,929 INFO 2026-06-08 09:12:06 MarkDuplicates Tracking 849232 as yet unmatched pairs. 59773 records in RAM. INFO 2026-06-08 09:12:08 MarkDuplicates Read 344,000,000 records. Elapsed time: 00:11:42s. Time for last 1,000,000: 2s. Last read position: chr11:64,287,819 INFO 2026-06-08 09:12:08 MarkDuplicates Tracking 846040 as yet unmatched pairs. 56533 records in RAM. INFO 2026-06-08 09:12:10 MarkDuplicates Read 345,000,000 records. Elapsed time: 00:11:44s. Time for last 1,000,000: 1s. Last read position: chr11:65,096,281 INFO 2026-06-08 09:12:10 MarkDuplicates Tracking 843035 as yet unmatched pairs. 53517 records in RAM. INFO 2026-06-08 09:12:12 MarkDuplicates Read 346,000,000 records. Elapsed time: 00:11:46s. Time for last 1,000,000: 2s. Last read position: chr11:65,554,336 INFO 2026-06-08 09:12:12 MarkDuplicates Tracking 840120 as yet unmatched pairs. 50427 records in RAM. INFO 2026-06-08 09:12:14 MarkDuplicates Read 347,000,000 records. Elapsed time: 00:11:48s. Time for last 1,000,000: 1s. Last read position: chr11:65,662,032 INFO 2026-06-08 09:12:14 MarkDuplicates Tracking 836511 as yet unmatched pairs. 46814 records in RAM. INFO 2026-06-08 09:12:16 MarkDuplicates Read 348,000,000 records. Elapsed time: 00:11:50s. Time for last 1,000,000: 2s. Last read position: chr11:66,315,593 INFO 2026-06-08 09:12:16 MarkDuplicates Tracking 833537 as yet unmatched pairs. 43814 records in RAM. INFO 2026-06-08 09:12:18 MarkDuplicates Read 349,000,000 records. Elapsed time: 00:11:52s. Time for last 1,000,000: 1s. Last read position: chr11:67,398,967 INFO 2026-06-08 09:12:18 MarkDuplicates Tracking 830131 as yet unmatched pairs. 40378 records in RAM. INFO 2026-06-08 09:12:20 MarkDuplicates Read 350,000,000 records. Elapsed time: 00:11:54s. Time for last 1,000,000: 1s. Last read position: chr11:69,005,866 INFO 2026-06-08 09:12:20 MarkDuplicates Tracking 827123 as yet unmatched pairs. 37342 records in RAM. INFO 2026-06-08 09:12:22 MarkDuplicates Read 351,000,000 records. Elapsed time: 00:11:56s. Time for last 1,000,000: 2s. Last read position: chr11:72,015,544 INFO 2026-06-08 09:12:22 MarkDuplicates Tracking 824233 as yet unmatched pairs. 34419 records in RAM. INFO 2026-06-08 09:12:24 MarkDuplicates Read 352,000,000 records. Elapsed time: 00:11:58s. Time for last 1,000,000: 1s. Last read position: chr11:73,679,677 INFO 2026-06-08 09:12:24 MarkDuplicates Tracking 820988 as yet unmatched pairs. 31157 records in RAM. INFO 2026-06-08 09:12:26 MarkDuplicates Read 353,000,000 records. Elapsed time: 00:12:00s. Time for last 1,000,000: 1s. Last read position: chr11:76,795,943 INFO 2026-06-08 09:12:26 MarkDuplicates Tracking 818142 as yet unmatched pairs. 28259 records in RAM. INFO 2026-06-08 09:12:28 MarkDuplicates Read 354,000,000 records. Elapsed time: 00:12:02s. Time for last 1,000,000: 2s. Last read position: chr11:78,854,219 INFO 2026-06-08 09:12:28 MarkDuplicates Tracking 815420 as yet unmatched pairs. 25472 records in RAM. INFO 2026-06-08 09:12:29 MarkDuplicates Read 355,000,000 records. Elapsed time: 00:12:03s. Time for last 1,000,000: 1s. Last read position: chr11:93,793,987 INFO 2026-06-08 09:12:29 MarkDuplicates Tracking 812709 as yet unmatched pairs. 22685 records in RAM. INFO 2026-06-08 09:12:31 MarkDuplicates Read 356,000,000 records. Elapsed time: 00:12:05s. Time for last 1,000,000: 1s. Last read position: chr11:99,033,382 INFO 2026-06-08 09:12:31 MarkDuplicates Tracking 809793 as yet unmatched pairs. 19741 records in RAM. INFO 2026-06-08 09:12:33 MarkDuplicates Read 357,000,000 records. Elapsed time: 00:12:07s. Time for last 1,000,000: 1s. Last read position: chr11:108,383,164 INFO 2026-06-08 09:12:33 MarkDuplicates Tracking 807310 as yet unmatched pairs. 17222 records in RAM. INFO 2026-06-08 09:12:35 MarkDuplicates Read 358,000,000 records. Elapsed time: 00:12:09s. Time for last 1,000,000: 2s. Last read position: chr11:117,408,899 INFO 2026-06-08 09:12:35 MarkDuplicates Tracking 804533 as yet unmatched pairs. 14398 records in RAM. INFO 2026-06-08 09:12:37 MarkDuplicates Read 359,000,000 records. Elapsed time: 00:12:11s. Time for last 1,000,000: 2s. Last read position: chr11:118,628,490 INFO 2026-06-08 09:12:37 MarkDuplicates Tracking 801885 as yet unmatched pairs. 11732 records in RAM. INFO 2026-06-08 09:12:39 MarkDuplicates Read 360,000,000 records. Elapsed time: 00:12:13s. Time for last 1,000,000: 1s. Last read position: chr11:119,419,493 INFO 2026-06-08 09:12:39 MarkDuplicates Tracking 799067 as yet unmatched pairs. 8871 records in RAM. INFO 2026-06-08 09:12:41 MarkDuplicates Read 361,000,000 records. Elapsed time: 00:12:15s. Time for last 1,000,000: 2s. Last read position: chr11:123,059,691 INFO 2026-06-08 09:12:41 MarkDuplicates Tracking 796695 as yet unmatched pairs. 6447 records in RAM. INFO 2026-06-08 09:12:43 MarkDuplicates Read 362,000,000 records. Elapsed time: 00:12:17s. Time for last 1,000,000: 1s. Last read position: chr11:128,694,254 INFO 2026-06-08 09:12:43 MarkDuplicates Tracking 793758 as yet unmatched pairs. 3466 records in RAM. INFO 2026-06-08 09:12:45 MarkDuplicates Read 363,000,000 records. Elapsed time: 00:12:19s. Time for last 1,000,000: 2s. Last read position: chr11:134,249,217 INFO 2026-06-08 09:12:45 MarkDuplicates Tracking 790455 as yet unmatched pairs. 89 records in RAM. INFO 2026-06-08 09:12:48 MarkDuplicates Read 364,000,000 records. Elapsed time: 00:12:22s. Time for last 1,000,000: 3s. Last read position: chr12:907,845 INFO 2026-06-08 09:12:48 MarkDuplicates Tracking 787977 as yet unmatched pairs. 104491 records in RAM. INFO 2026-06-08 09:12:50 MarkDuplicates Read 365,000,000 records. Elapsed time: 00:12:24s. Time for last 1,000,000: 1s. Last read position: chr12:4,351,281 INFO 2026-06-08 09:12:50 MarkDuplicates Tracking 784800 as yet unmatched pairs. 101262 records in RAM. INFO 2026-06-08 09:12:52 MarkDuplicates Read 366,000,000 records. Elapsed time: 00:12:26s. Time for last 1,000,000: 2s. Last read position: chr12:6,697,694 INFO 2026-06-08 09:12:52 MarkDuplicates Tracking 781930 as yet unmatched pairs. 98368 records in RAM. INFO 2026-06-08 09:12:54 MarkDuplicates Read 367,000,000 records. Elapsed time: 00:12:28s. Time for last 1,000,000: 1s. Last read position: chr12:6,940,903 INFO 2026-06-08 09:12:54 MarkDuplicates Tracking 779364 as yet unmatched pairs. 95787 records in RAM. INFO 2026-06-08 09:12:56 MarkDuplicates Read 368,000,000 records. Elapsed time: 00:12:30s. Time for last 1,000,000: 2s. Last read position: chr12:8,932,853 INFO 2026-06-08 09:12:56 MarkDuplicates Tracking 776608 as yet unmatched pairs. 93001 records in RAM. INFO 2026-06-08 09:12:58 MarkDuplicates Read 369,000,000 records. Elapsed time: 00:12:32s. Time for last 1,000,000: 2s. Last read position: chr12:11,839,279 INFO 2026-06-08 09:12:58 MarkDuplicates Tracking 774675 as yet unmatched pairs. 91034 records in RAM. INFO 2026-06-08 09:13:00 MarkDuplicates Read 370,000,000 records. Elapsed time: 00:12:34s. Time for last 1,000,000: 2s. Last read position: chr12:14,882,178 INFO 2026-06-08 09:13:00 MarkDuplicates Tracking 772311 as yet unmatched pairs. 88642 records in RAM. INFO 2026-06-08 09:13:02 MarkDuplicates Read 371,000,000 records. Elapsed time: 00:12:36s. Time for last 1,000,000: 2s. Last read position: chr12:27,650,139 INFO 2026-06-08 09:13:02 MarkDuplicates Tracking 769290 as yet unmatched pairs. 85564 records in RAM. INFO 2026-06-08 09:13:04 MarkDuplicates Read 372,000,000 records. Elapsed time: 00:12:38s. Time for last 1,000,000: 2s. Last read position: chr12:40,993,117 INFO 2026-06-08 09:13:04 MarkDuplicates Tracking 766566 as yet unmatched pairs. 82780 records in RAM. INFO 2026-06-08 09:13:07 MarkDuplicates Read 373,000,000 records. Elapsed time: 00:12:41s. Time for last 1,000,000: 2s. Last read position: chr12:48,347,988 INFO 2026-06-08 09:13:07 MarkDuplicates Tracking 763944 as yet unmatched pairs. 80117 records in RAM. INFO 2026-06-08 09:13:09 MarkDuplicates Read 374,000,000 records. Elapsed time: 00:12:43s. Time for last 1,000,000: 2s. Last read position: chr12:49,050,587 INFO 2026-06-08 09:13:09 MarkDuplicates Tracking 761186 as yet unmatched pairs. 77329 records in RAM. INFO 2026-06-08 09:13:11 MarkDuplicates Read 375,000,000 records. Elapsed time: 00:12:45s. Time for last 1,000,000: 1s. Last read position: chr12:49,524,836 INFO 2026-06-08 09:13:11 MarkDuplicates Tracking 758788 as yet unmatched pairs. 74912 records in RAM. INFO 2026-06-08 09:13:13 MarkDuplicates Read 376,000,000 records. Elapsed time: 00:12:47s. Time for last 1,000,000: 2s. Last read position: chr12:51,109,177 INFO 2026-06-08 09:13:13 MarkDuplicates Tracking 756317 as yet unmatched pairs. 72406 records in RAM. INFO 2026-06-08 09:13:15 MarkDuplicates Read 377,000,000 records. Elapsed time: 00:12:49s. Time for last 1,000,000: 1s. Last read position: chr12:53,057,659 INFO 2026-06-08 09:13:15 MarkDuplicates Tracking 753007 as yet unmatched pairs. 69071 records in RAM. INFO 2026-06-08 09:13:17 MarkDuplicates Read 378,000,000 records. Elapsed time: 00:12:51s. Time for last 1,000,000: 2s. Last read position: chr12:53,483,939 INFO 2026-06-08 09:13:17 MarkDuplicates Tracking 750278 as yet unmatched pairs. 66313 records in RAM. INFO 2026-06-08 09:13:19 MarkDuplicates Read 379,000,000 records. Elapsed time: 00:12:53s. Time for last 1,000,000: 2s. Last read position: chr12:54,282,596 INFO 2026-06-08 09:13:19 MarkDuplicates Tracking 748257 as yet unmatched pairs. 64270 records in RAM. INFO 2026-06-08 09:13:21 MarkDuplicates Read 380,000,000 records. Elapsed time: 00:12:55s. Time for last 1,000,000: 1s. Last read position: chr12:55,716,088 INFO 2026-06-08 09:13:21 MarkDuplicates Tracking 745336 as yet unmatched pairs. 61324 records in RAM. INFO 2026-06-08 09:13:23 MarkDuplicates Read 381,000,000 records. Elapsed time: 00:12:57s. Time for last 1,000,000: 2s. Last read position: chr12:56,245,530 INFO 2026-06-08 09:13:23 MarkDuplicates Tracking 742608 as yet unmatched pairs. 58580 records in RAM. INFO 2026-06-08 09:13:25 MarkDuplicates Read 382,000,000 records. Elapsed time: 00:12:59s. Time for last 1,000,000: 1s. Last read position: chr12:56,718,782 INFO 2026-06-08 09:13:25 MarkDuplicates Tracking 740059 as yet unmatched pairs. 56000 records in RAM. INFO 2026-06-08 09:13:27 MarkDuplicates Read 383,000,000 records. Elapsed time: 00:13:01s. Time for last 1,000,000: 2s. Last read position: chr12:57,104,491 INFO 2026-06-08 09:13:27 MarkDuplicates Tracking 738765 as yet unmatched pairs. 54700 records in RAM. INFO 2026-06-08 09:13:29 MarkDuplicates Read 384,000,000 records. Elapsed time: 00:13:03s. Time for last 1,000,000: 2s. Last read position: chr12:57,184,092 INFO 2026-06-08 09:13:29 MarkDuplicates Tracking 734309 as yet unmatched pairs. 50232 records in RAM. INFO 2026-06-08 09:13:31 MarkDuplicates Read 385,000,000 records. Elapsed time: 00:13:05s. Time for last 1,000,000: 1s. Last read position: chr12:57,284,005 INFO 2026-06-08 09:13:31 MarkDuplicates Tracking 731208 as yet unmatched pairs. 47110 records in RAM. INFO 2026-06-08 09:13:33 MarkDuplicates Read 386,000,000 records. Elapsed time: 00:13:07s. Time for last 1,000,000: 2s. Last read position: chr12:57,525,766 INFO 2026-06-08 09:13:33 MarkDuplicates Tracking 728337 as yet unmatched pairs. 44216 records in RAM. INFO 2026-06-08 09:13:34 MarkDuplicates Read 387,000,000 records. Elapsed time: 00:13:08s. Time for last 1,000,000: 1s. Last read position: chr12:58,877,626 INFO 2026-06-08 09:13:34 MarkDuplicates Tracking 725307 as yet unmatched pairs. 41156 records in RAM. INFO 2026-06-08 09:13:37 MarkDuplicates Read 388,000,000 records. Elapsed time: 00:13:11s. Time for last 1,000,000: 2s. Last read position: chr12:67,306,563 INFO 2026-06-08 09:13:37 MarkDuplicates Tracking 722567 as yet unmatched pairs. 38356 records in RAM. INFO 2026-06-08 09:13:39 MarkDuplicates Read 389,000,000 records. Elapsed time: 00:13:13s. Time for last 1,000,000: 2s. Last read position: chr12:76,030,776 INFO 2026-06-08 09:13:39 MarkDuplicates Tracking 720268 as yet unmatched pairs. 36036 records in RAM. INFO 2026-06-08 09:13:41 MarkDuplicates Read 390,000,000 records. Elapsed time: 00:13:15s. Time for last 1,000,000: 1s. Last read position: chr12:89,349,348 INFO 2026-06-08 09:13:41 MarkDuplicates Tracking 717536 as yet unmatched pairs. 33227 records in RAM. INFO 2026-06-08 09:13:43 MarkDuplicates Read 391,000,000 records. Elapsed time: 00:13:17s. Time for last 1,000,000: 2s. Last read position: chr12:96,029,172 INFO 2026-06-08 09:13:43 MarkDuplicates Tracking 714927 as yet unmatched pairs. 30595 records in RAM. INFO 2026-06-08 09:13:45 MarkDuplicates Read 392,000,000 records. Elapsed time: 00:13:19s. Time for last 1,000,000: 2s. Last read position: chr12:102,480,424 INFO 2026-06-08 09:13:45 MarkDuplicates Tracking 712305 as yet unmatched pairs. 27933 records in RAM. INFO 2026-06-08 09:13:46 MarkDuplicates Read 393,000,000 records. Elapsed time: 00:13:20s. Time for last 1,000,000: 1s. Last read position: chr12:108,525,510 INFO 2026-06-08 09:13:46 MarkDuplicates Tracking 709657 as yet unmatched pairs. 25246 records in RAM. INFO 2026-06-08 09:13:49 MarkDuplicates Read 394,000,000 records. Elapsed time: 00:13:23s. Time for last 1,000,000: 2s. Last read position: chr12:111,519,988 INFO 2026-06-08 09:13:49 MarkDuplicates Tracking 706847 as yet unmatched pairs. 22407 records in RAM. INFO 2026-06-08 09:13:50 MarkDuplicates Read 395,000,000 records. Elapsed time: 00:13:24s. Time for last 1,000,000: 1s. Last read position: chr12:113,948,972 INFO 2026-06-08 09:13:50 MarkDuplicates Tracking 704005 as yet unmatched pairs. 19520 records in RAM. INFO 2026-06-08 09:13:53 MarkDuplicates Read 396,000,000 records. Elapsed time: 00:13:27s. Time for last 1,000,000: 2s. Last read position: chr12:120,196,920 INFO 2026-06-08 09:13:53 MarkDuplicates Tracking 701656 as yet unmatched pairs. 17152 records in RAM. INFO 2026-06-08 09:13:55 MarkDuplicates Read 397,000,000 records. Elapsed time: 00:13:29s. Time for last 1,000,000: 2s. Last read position: chr12:122,133,497 INFO 2026-06-08 09:13:55 MarkDuplicates Tracking 697964 as yet unmatched pairs. 13447 records in RAM. INFO 2026-06-08 09:13:57 MarkDuplicates Read 398,000,000 records. Elapsed time: 00:13:31s. Time for last 1,000,000: 2s. Last read position: chr12:123,937,102 INFO 2026-06-08 09:13:57 MarkDuplicates Tracking 695217 as yet unmatched pairs. 10675 records in RAM. INFO 2026-06-08 09:13:59 MarkDuplicates Read 399,000,000 records. Elapsed time: 00:13:33s. Time for last 1,000,000: 2s. Last read position: chr12:124,372,262 INFO 2026-06-08 09:13:59 MarkDuplicates Tracking 692217 as yet unmatched pairs. 7658 records in RAM. INFO 2026-06-08 09:14:01 MarkDuplicates Read 400,000,000 records. Elapsed time: 00:13:35s. Time for last 1,000,000: 1s. Last read position: chr12:131,932,184 INFO 2026-06-08 09:14:01 MarkDuplicates Tracking 689137 as yet unmatched pairs. 4546 records in RAM. INFO 2026-06-08 09:14:03 MarkDuplicates Read 401,000,000 records. Elapsed time: 00:13:37s. Time for last 1,000,000: 2s. Last read position: chr12:132,786,481 INFO 2026-06-08 09:14:03 MarkDuplicates Tracking 685894 as yet unmatched pairs. 1296 records in RAM. INFO 2026-06-08 09:14:06 MarkDuplicates Read 402,000,000 records. Elapsed time: 00:13:40s. Time for last 1,000,000: 2s. Last read position: chr13:20,058,581 INFO 2026-06-08 09:14:06 MarkDuplicates Tracking 684299 as yet unmatched pairs. 34772 records in RAM. INFO 2026-06-08 09:14:08 MarkDuplicates Read 403,000,000 records. Elapsed time: 00:13:42s. Time for last 1,000,000: 1s. Last read position: chr13:26,215,219 INFO 2026-06-08 09:14:08 MarkDuplicates Tracking 680752 as yet unmatched pairs. 31205 records in RAM. INFO 2026-06-08 09:14:10 MarkDuplicates Read 404,000,000 records. Elapsed time: 00:13:44s. Time for last 1,000,000: 2s. Last read position: chr13:32,675,894 INFO 2026-06-08 09:14:10 MarkDuplicates Tracking 678336 as yet unmatched pairs. 28746 records in RAM. INFO 2026-06-08 09:14:12 MarkDuplicates Read 405,000,000 records. Elapsed time: 00:13:46s. Time for last 1,000,000: 1s. Last read position: chr13:37,577,753 INFO 2026-06-08 09:14:12 MarkDuplicates Tracking 676913 as yet unmatched pairs. 27266 records in RAM. INFO 2026-06-08 09:14:14 MarkDuplicates Read 406,000,000 records. Elapsed time: 00:13:48s. Time for last 1,000,000: 2s. Last read position: chr13:41,336,738 INFO 2026-06-08 09:14:14 MarkDuplicates Tracking 673173 as yet unmatched pairs. 23496 records in RAM. INFO 2026-06-08 09:14:16 MarkDuplicates Read 407,000,000 records. Elapsed time: 00:13:50s. Time for last 1,000,000: 2s. Last read position: chr13:45,975,435 INFO 2026-06-08 09:14:16 MarkDuplicates Tracking 670397 as yet unmatched pairs. 20688 records in RAM. INFO 2026-06-08 09:14:18 MarkDuplicates Read 408,000,000 records. Elapsed time: 00:13:52s. Time for last 1,000,000: 1s. Last read position: chr13:52,415,752 INFO 2026-06-08 09:14:18 MarkDuplicates Tracking 667959 as yet unmatched pairs. 18220 records in RAM. INFO 2026-06-08 09:14:20 MarkDuplicates Read 409,000,000 records. Elapsed time: 00:13:54s. Time for last 1,000,000: 1s. Last read position: chr13:75,853,133 INFO 2026-06-08 09:14:20 MarkDuplicates Tracking 665330 as yet unmatched pairs. 15552 records in RAM. INFO 2026-06-08 09:14:22 MarkDuplicates Read 410,000,000 records. Elapsed time: 00:13:56s. Time for last 1,000,000: 1s. Last read position: chr13:95,589,156 INFO 2026-06-08 09:14:22 MarkDuplicates Tracking 662739 as yet unmatched pairs. 12826 records in RAM. INFO 2026-06-08 09:14:24 MarkDuplicates Read 411,000,000 records. Elapsed time: 00:13:58s. Time for last 1,000,000: 2s. Last read position: chr13:102,147,712 INFO 2026-06-08 09:14:24 MarkDuplicates Tracking 659495 as yet unmatched pairs. 9516 records in RAM. INFO 2026-06-08 09:14:26 MarkDuplicates Read 412,000,000 records. Elapsed time: 00:14:00s. Time for last 1,000,000: 2s. Last read position: chr13:110,207,402 INFO 2026-06-08 09:14:26 MarkDuplicates Tracking 656928 as yet unmatched pairs. 6920 records in RAM. INFO 2026-06-08 09:14:27 MarkDuplicates Read 413,000,000 records. Elapsed time: 00:14:01s. Time for last 1,000,000: 1s. Last read position: chr13:110,506,498 INFO 2026-06-08 09:14:27 MarkDuplicates Tracking 653851 as yet unmatched pairs. 3810 records in RAM. INFO 2026-06-08 09:14:30 MarkDuplicates Read 414,000,000 records. Elapsed time: 00:14:04s. Time for last 1,000,000: 2s. Last read position: chr13:114,324,862 INFO 2026-06-08 09:14:30 MarkDuplicates Tracking 650307 as yet unmatched pairs. 221 records in RAM. INFO 2026-06-08 09:14:32 MarkDuplicates Read 415,000,000 records. Elapsed time: 00:14:06s. Time for last 1,000,000: 2s. Last read position: chr14:21,087,451 INFO 2026-06-08 09:14:32 MarkDuplicates Tracking 647493 as yet unmatched pairs. 55435 records in RAM. INFO 2026-06-08 09:14:35 MarkDuplicates Read 416,000,000 records. Elapsed time: 00:14:09s. Time for last 1,000,000: 2s. Last read position: chr14:22,841,926 INFO 2026-06-08 09:14:35 MarkDuplicates Tracking 644495 as yet unmatched pairs. 52403 records in RAM. INFO 2026-06-08 09:14:38 MarkDuplicates Read 417,000,000 records. Elapsed time: 00:14:12s. Time for last 1,000,000: 2s. Last read position: chr14:23,080,299 INFO 2026-06-08 09:14:38 MarkDuplicates Tracking 641888 as yet unmatched pairs. 49789 records in RAM. INFO 2026-06-08 09:14:39 MarkDuplicates Read 418,000,000 records. Elapsed time: 00:14:13s. Time for last 1,000,000: 1s. Last read position: chr14:24,193,242 INFO 2026-06-08 09:14:39 MarkDuplicates Tracking 638340 as yet unmatched pairs. 46225 records in RAM. INFO 2026-06-08 09:14:41 MarkDuplicates Read 419,000,000 records. Elapsed time: 00:14:15s. Time for last 1,000,000: 1s. Last read position: chr14:27,505,461 INFO 2026-06-08 09:14:41 MarkDuplicates Tracking 635292 as yet unmatched pairs. 43147 records in RAM. INFO 2026-06-08 09:14:43 MarkDuplicates Read 420,000,000 records. Elapsed time: 00:14:17s. Time for last 1,000,000: 1s. Last read position: chr14:35,123,521 INFO 2026-06-08 09:14:43 MarkDuplicates Tracking 632704 as yet unmatched pairs. 40486 records in RAM. INFO 2026-06-08 09:14:45 MarkDuplicates Read 421,000,000 records. Elapsed time: 00:14:19s. Time for last 1,000,000: 2s. Last read position: chr14:49,586,642 INFO 2026-06-08 09:14:45 MarkDuplicates Tracking 630220 as yet unmatched pairs. 37966 records in RAM. INFO 2026-06-08 09:14:47 MarkDuplicates Read 422,000,000 records. Elapsed time: 00:14:21s. Time for last 1,000,000: 1s. Last read position: chr14:52,054,250 INFO 2026-06-08 09:14:47 MarkDuplicates Tracking 627911 as yet unmatched pairs. 35627 records in RAM. INFO 2026-06-08 09:14:49 MarkDuplicates Read 423,000,000 records. Elapsed time: 00:14:23s. Time for last 1,000,000: 2s. Last read position: chr14:58,638,232 INFO 2026-06-08 09:14:49 MarkDuplicates Tracking 624920 as yet unmatched pairs. 32615 records in RAM. INFO 2026-06-08 09:14:51 MarkDuplicates Read 424,000,000 records. Elapsed time: 00:14:25s. Time for last 1,000,000: 2s. Last read position: chr14:63,990,937 INFO 2026-06-08 09:14:51 MarkDuplicates Tracking 622226 as yet unmatched pairs. 29891 records in RAM. INFO 2026-06-08 09:14:53 MarkDuplicates Read 425,000,000 records. Elapsed time: 00:14:27s. Time for last 1,000,000: 1s. Last read position: chr14:67,806,621 INFO 2026-06-08 09:14:53 MarkDuplicates Tracking 619523 as yet unmatched pairs. 27159 records in RAM. INFO 2026-06-08 09:14:55 MarkDuplicates Read 426,000,000 records. Elapsed time: 00:14:29s. Time for last 1,000,000: 1s. Last read position: chr14:71,033,516 INFO 2026-06-08 09:14:55 MarkDuplicates Tracking 616742 as yet unmatched pairs. 24361 records in RAM. INFO 2026-06-08 09:14:57 MarkDuplicates Read 427,000,000 records. Elapsed time: 00:14:31s. Time for last 1,000,000: 1s. Last read position: chr14:74,763,659 INFO 2026-06-08 09:14:57 MarkDuplicates Tracking 614051 as yet unmatched pairs. 21644 records in RAM. INFO 2026-06-08 09:14:59 MarkDuplicates Read 428,000,000 records. Elapsed time: 00:14:33s. Time for last 1,000,000: 1s. Last read position: chr14:75,280,619 INFO 2026-06-08 09:14:59 MarkDuplicates Tracking 612272 as yet unmatched pairs. 19837 records in RAM. INFO 2026-06-08 09:15:00 MarkDuplicates Read 429,000,000 records. Elapsed time: 00:14:34s. Time for last 1,000,000: 1s. Last read position: chr14:85,621,802 INFO 2026-06-08 09:15:00 MarkDuplicates Tracking 608340 as yet unmatched pairs. 15855 records in RAM. INFO 2026-06-08 09:15:02 MarkDuplicates Read 430,000,000 records. Elapsed time: 00:14:36s. Time for last 1,000,000: 2s. Last read position: chr14:92,026,865 INFO 2026-06-08 09:15:02 MarkDuplicates Tracking 605491 as yet unmatched pairs. 12971 records in RAM. INFO 2026-06-08 09:15:04 MarkDuplicates Read 431,000,000 records. Elapsed time: 00:14:38s. Time for last 1,000,000: 2s. Last read position: chr14:99,502,964 INFO 2026-06-08 09:15:04 MarkDuplicates Tracking 602879 as yet unmatched pairs. 10297 records in RAM. INFO 2026-06-08 09:15:06 MarkDuplicates Read 432,000,000 records. Elapsed time: 00:14:40s. Time for last 1,000,000: 1s. Last read position: chr14:102,016,817 INFO 2026-06-08 09:15:06 MarkDuplicates Tracking 600036 as yet unmatched pairs. 7431 records in RAM. INFO 2026-06-08 09:15:08 MarkDuplicates Read 433,000,000 records. Elapsed time: 00:14:42s. Time for last 1,000,000: 2s. Last read position: chr14:103,338,333 INFO 2026-06-08 09:15:08 MarkDuplicates Tracking 596822 as yet unmatched pairs. 4191 records in RAM. INFO 2026-06-08 09:15:10 MarkDuplicates Read 434,000,000 records. Elapsed time: 00:14:44s. Time for last 1,000,000: 1s. Last read position: chr14:105,348,502 INFO 2026-06-08 09:15:10 MarkDuplicates Tracking 593821 as yet unmatched pairs. 1169 records in RAM. INFO 2026-06-08 09:15:13 MarkDuplicates Read 435,000,000 records. Elapsed time: 00:14:47s. Time for last 1,000,000: 2s. Last read position: chr15:24,978,428 INFO 2026-06-08 09:15:13 MarkDuplicates Tracking 591245 as yet unmatched pairs. 59032 records in RAM. INFO 2026-06-08 09:15:14 MarkDuplicates Read 436,000,000 records. Elapsed time: 00:14:48s. Time for last 1,000,000: 1s. Last read position: chr15:29,719,082 INFO 2026-06-08 09:15:14 MarkDuplicates Tracking 589502 as yet unmatched pairs. 57260 records in RAM. INFO 2026-06-08 09:15:16 MarkDuplicates Read 437,000,000 records. Elapsed time: 00:14:50s. Time for last 1,000,000: 1s. Last read position: chr15:33,812,974 INFO 2026-06-08 09:15:16 MarkDuplicates Tracking 587038 as yet unmatched pairs. 54759 records in RAM. INFO 2026-06-08 09:15:18 MarkDuplicates Read 438,000,000 records. Elapsed time: 00:14:52s. Time for last 1,000,000: 1s. Last read position: chr15:34,534,146 INFO 2026-06-08 09:15:18 MarkDuplicates Tracking 585075 as yet unmatched pairs. 52783 records in RAM. INFO 2026-06-08 09:15:20 MarkDuplicates Read 439,000,000 records. Elapsed time: 00:14:54s. Time for last 1,000,000: 2s. Last read position: chr15:41,371,590 INFO 2026-06-08 09:15:20 MarkDuplicates Tracking 582436 as yet unmatched pairs. 50106 records in RAM. INFO 2026-06-08 09:15:22 MarkDuplicates Read 440,000,000 records. Elapsed time: 00:14:56s. Time for last 1,000,000: 2s. Last read position: chr15:42,351,366 INFO 2026-06-08 09:15:22 MarkDuplicates Tracking 579762 as yet unmatched pairs. 47400 records in RAM. INFO 2026-06-08 09:15:24 MarkDuplicates Read 441,000,000 records. Elapsed time: 00:14:58s. Time for last 1,000,000: 1s. Last read position: chr15:43,527,568 INFO 2026-06-08 09:15:24 MarkDuplicates Tracking 577006 as yet unmatched pairs. 44629 records in RAM. INFO 2026-06-08 09:15:26 MarkDuplicates Read 442,000,000 records. Elapsed time: 00:15:00s. Time for last 1,000,000: 2s. Last read position: chr15:48,487,087 INFO 2026-06-08 09:15:26 MarkDuplicates Tracking 574331 as yet unmatched pairs. 41943 records in RAM. INFO 2026-06-08 09:15:28 MarkDuplicates Read 443,000,000 records. Elapsed time: 00:15:02s. Time for last 1,000,000: 1s. Last read position: chr15:55,185,362 INFO 2026-06-08 09:15:28 MarkDuplicates Tracking 571706 as yet unmatched pairs. 39289 records in RAM. INFO 2026-06-08 09:15:30 MarkDuplicates Read 444,000,000 records. Elapsed time: 00:15:04s. Time for last 1,000,000: 2s. Last read position: chr15:57,232,800 INFO 2026-06-08 09:15:30 MarkDuplicates Tracking 570247 as yet unmatched pairs. 37800 records in RAM. INFO 2026-06-08 09:15:32 MarkDuplicates Read 445,000,000 records. Elapsed time: 00:15:06s. Time for last 1,000,000: 2s. Last read position: chr15:61,961,755 INFO 2026-06-08 09:15:32 MarkDuplicates Tracking 566726 as yet unmatched pairs. 34246 records in RAM. INFO 2026-06-08 09:15:34 MarkDuplicates Read 446,000,000 records. Elapsed time: 00:15:08s. Time for last 1,000,000: 1s. Last read position: chr15:64,688,779 INFO 2026-06-08 09:15:34 MarkDuplicates Tracking 563858 as yet unmatched pairs. 31351 records in RAM. INFO 2026-06-08 09:15:36 MarkDuplicates Read 447,000,000 records. Elapsed time: 00:15:10s. Time for last 1,000,000: 2s. Last read position: chr15:67,066,264 INFO 2026-06-08 09:15:36 MarkDuplicates Tracking 560914 as yet unmatched pairs. 28383 records in RAM. INFO 2026-06-08 09:15:38 MarkDuplicates Read 448,000,000 records. Elapsed time: 00:15:12s. Time for last 1,000,000: 1s. Last read position: chr15:71,242,927 INFO 2026-06-08 09:15:38 MarkDuplicates Tracking 558145 as yet unmatched pairs. 25588 records in RAM. INFO 2026-06-08 09:15:40 MarkDuplicates Read 449,000,000 records. Elapsed time: 00:15:14s. Time for last 1,000,000: 2s. Last read position: chr15:73,998,334 INFO 2026-06-08 09:15:40 MarkDuplicates Tracking 555275 as yet unmatched pairs. 22686 records in RAM. INFO 2026-06-08 09:15:41 MarkDuplicates Read 450,000,000 records. Elapsed time: 00:15:15s. Time for last 1,000,000: 1s. Last read position: chr15:75,490,209 INFO 2026-06-08 09:15:41 MarkDuplicates Tracking 552438 as yet unmatched pairs. 19833 records in RAM. INFO 2026-06-08 09:15:43 MarkDuplicates Read 451,000,000 records. Elapsed time: 00:15:17s. Time for last 1,000,000: 1s. Last read position: chr15:77,181,778 INFO 2026-06-08 09:15:43 MarkDuplicates Tracking 550343 as yet unmatched pairs. 17718 records in RAM. INFO 2026-06-08 09:15:45 MarkDuplicates Read 452,000,000 records. Elapsed time: 00:15:19s. Time for last 1,000,000: 2s. Last read position: chr15:79,889,339 INFO 2026-06-08 09:15:45 MarkDuplicates Tracking 546388 as yet unmatched pairs. 13727 records in RAM. INFO 2026-06-08 09:15:47 MarkDuplicates Read 453,000,000 records. Elapsed time: 00:15:21s. Time for last 1,000,000: 1s. Last read position: chr15:84,643,571 INFO 2026-06-08 09:15:47 MarkDuplicates Tracking 544366 as yet unmatched pairs. 11689 records in RAM. INFO 2026-06-08 09:15:49 MarkDuplicates Read 454,000,000 records. Elapsed time: 00:15:23s. Time for last 1,000,000: 1s. Last read position: chr15:88,032,903 INFO 2026-06-08 09:15:49 MarkDuplicates Tracking 543433 as yet unmatched pairs. 10740 records in RAM. INFO 2026-06-08 09:15:51 MarkDuplicates Read 455,000,000 records. Elapsed time: 00:15:25s. Time for last 1,000,000: 1s. Last read position: chr15:90,473,727 INFO 2026-06-08 09:15:51 MarkDuplicates Tracking 538939 as yet unmatched pairs. 6234 records in RAM. INFO 2026-06-08 09:15:53 MarkDuplicates Read 456,000,000 records. Elapsed time: 00:15:27s. Time for last 1,000,000: 2s. Last read position: chr15:96,334,148 INFO 2026-06-08 09:15:53 MarkDuplicates Tracking 537254 as yet unmatched pairs. 4521 records in RAM. INFO 2026-06-08 09:15:55 MarkDuplicates Read 457,000,000 records. Elapsed time: 00:15:29s. Time for last 1,000,000: 1s. Last read position: chr15:101,974,251 INFO 2026-06-08 09:15:55 MarkDuplicates Tracking 532806 as yet unmatched pairs. 31 records in RAM. INFO 2026-06-08 09:15:58 MarkDuplicates Read 458,000,000 records. Elapsed time: 00:15:32s. Time for last 1,000,000: 2s. Last read position: chr16:673,088 INFO 2026-06-08 09:15:58 MarkDuplicates Tracking 529788 as yet unmatched pairs. 87180 records in RAM. INFO 2026-06-08 09:16:00 MarkDuplicates Read 459,000,000 records. Elapsed time: 00:15:34s. Time for last 1,000,000: 2s. Last read position: chr16:1,773,419 INFO 2026-06-08 09:16:00 MarkDuplicates Tracking 525945 as yet unmatched pairs. 83321 records in RAM. INFO 2026-06-08 09:16:01 MarkDuplicates Read 460,000,000 records. Elapsed time: 00:15:35s. Time for last 1,000,000: 1s. Last read position: chr16:2,115,597 INFO 2026-06-08 09:16:01 MarkDuplicates Tracking 522436 as yet unmatched pairs. 79799 records in RAM. INFO 2026-06-08 09:16:03 MarkDuplicates Read 461,000,000 records. Elapsed time: 00:15:37s. Time for last 1,000,000: 2s. Last read position: chr16:2,762,418 INFO 2026-06-08 09:16:03 MarkDuplicates Tracking 519726 as yet unmatched pairs. 77075 records in RAM. INFO 2026-06-08 09:16:05 MarkDuplicates Read 462,000,000 records. Elapsed time: 00:15:39s. Time for last 1,000,000: 1s. Last read position: chr16:2,767,273 INFO 2026-06-08 09:16:05 MarkDuplicates Tracking 516933 as yet unmatched pairs. 74269 records in RAM. INFO 2026-06-08 09:16:07 MarkDuplicates Read 463,000,000 records. Elapsed time: 00:15:41s. Time for last 1,000,000: 2s. Last read position: chr16:3,728,973 INFO 2026-06-08 09:16:07 MarkDuplicates Tracking 513549 as yet unmatched pairs. 70875 records in RAM. INFO 2026-06-08 09:16:09 MarkDuplicates Read 464,000,000 records. Elapsed time: 00:15:43s. Time for last 1,000,000: 1s. Last read position: chr16:5,078,793 INFO 2026-06-08 09:16:09 MarkDuplicates Tracking 510325 as yet unmatched pairs. 67636 records in RAM. INFO 2026-06-08 09:16:11 MarkDuplicates Read 465,000,000 records. Elapsed time: 00:15:45s. Time for last 1,000,000: 2s. Last read position: chr16:14,245,557 INFO 2026-06-08 09:16:11 MarkDuplicates Tracking 508248 as yet unmatched pairs. 65531 records in RAM. INFO 2026-06-08 09:16:13 MarkDuplicates Read 466,000,000 records. Elapsed time: 00:15:47s. Time for last 1,000,000: 1s. Last read position: chr16:14,928,383 INFO 2026-06-08 09:16:13 MarkDuplicates Tracking 506364 as yet unmatched pairs. 63638 records in RAM. INFO 2026-06-08 09:16:14 MarkDuplicates Read 467,000,000 records. Elapsed time: 00:15:48s. Time for last 1,000,000: 1s. Last read position: chr16:15,366,519 INFO 2026-06-08 09:16:14 MarkDuplicates Tracking 504884 as yet unmatched pairs. 62148 records in RAM. INFO 2026-06-08 09:16:16 MarkDuplicates Read 468,000,000 records. Elapsed time: 00:15:50s. Time for last 1,000,000: 1s. Last read position: chr16:16,329,451 INFO 2026-06-08 09:16:16 MarkDuplicates Tracking 503428 as yet unmatched pairs. 60678 records in RAM. INFO 2026-06-08 09:16:18 MarkDuplicates Read 469,000,000 records. Elapsed time: 00:15:52s. Time for last 1,000,000: 1s. Last read position: chr16:17,259,145 INFO 2026-06-08 09:16:18 MarkDuplicates Tracking 502742 as yet unmatched pairs. 59989 records in RAM. INFO 2026-06-08 09:16:19 MarkDuplicates Read 470,000,000 records. Elapsed time: 00:15:53s. Time for last 1,000,000: 1s. Last read position: chr16:18,364,253 INFO 2026-06-08 09:16:19 MarkDuplicates Tracking 502133 as yet unmatched pairs. 59369 records in RAM. INFO 2026-06-08 09:16:21 MarkDuplicates Read 471,000,000 records. Elapsed time: 00:15:55s. Time for last 1,000,000: 1s. Last read position: chr16:19,115,339 INFO 2026-06-08 09:16:21 MarkDuplicates Tracking 499962 as yet unmatched pairs. 57186 records in RAM. INFO 2026-06-08 09:16:22 MarkDuplicates Read 472,000,000 records. Elapsed time: 00:15:56s. Time for last 1,000,000: 1s. Last read position: chr16:21,455,477 INFO 2026-06-08 09:16:22 MarkDuplicates Tracking 498675 as yet unmatched pairs. 55892 records in RAM. INFO 2026-06-08 09:16:24 MarkDuplicates Read 473,000,000 records. Elapsed time: 00:15:58s. Time for last 1,000,000: 1s. Last read position: chr16:22,300,710 INFO 2026-06-08 09:16:24 MarkDuplicates Tracking 497406 as yet unmatched pairs. 54611 records in RAM. INFO 2026-06-08 09:16:26 MarkDuplicates Read 474,000,000 records. Elapsed time: 00:16:00s. Time for last 1,000,000: 1s. Last read position: chr16:23,068,886 INFO 2026-06-08 09:16:26 MarkDuplicates Tracking 496698 as yet unmatched pairs. 53897 records in RAM. INFO 2026-06-08 09:16:27 MarkDuplicates Read 475,000,000 records. Elapsed time: 00:16:01s. Time for last 1,000,000: 1s. Last read position: chr16:28,117,384 INFO 2026-06-08 09:16:27 MarkDuplicates Tracking 494060 as yet unmatched pairs. 51243 records in RAM. INFO 2026-06-08 09:16:29 MarkDuplicates Read 476,000,000 records. Elapsed time: 00:16:03s. Time for last 1,000,000: 1s. Last read position: chr16:28,843,024 INFO 2026-06-08 09:16:29 MarkDuplicates Tracking 491689 as yet unmatched pairs. 48864 records in RAM. INFO 2026-06-08 09:16:31 MarkDuplicates Read 477,000,000 records. Elapsed time: 00:16:05s. Time for last 1,000,000: 1s. Last read position: chr16:29,484,880 INFO 2026-06-08 09:16:31 MarkDuplicates Tracking 490710 as yet unmatched pairs. 47880 records in RAM. INFO 2026-06-08 09:16:33 MarkDuplicates Read 478,000,000 records. Elapsed time: 00:16:07s. Time for last 1,000,000: 1s. Last read position: chr16:29,990,803 INFO 2026-06-08 09:16:33 MarkDuplicates Tracking 488283 as yet unmatched pairs. 45444 records in RAM. INFO 2026-06-08 09:16:34 MarkDuplicates Read 479,000,000 records. Elapsed time: 00:16:08s. Time for last 1,000,000: 1s. Last read position: chr16:30,398,228 INFO 2026-06-08 09:16:34 MarkDuplicates Tracking 486898 as yet unmatched pairs. 44049 records in RAM. INFO 2026-06-08 09:16:36 MarkDuplicates Read 480,000,000 records. Elapsed time: 00:16:10s. Time for last 1,000,000: 1s. Last read position: chr16:30,782,005 INFO 2026-06-08 09:16:36 MarkDuplicates Tracking 483941 as yet unmatched pairs. 41071 records in RAM. INFO 2026-06-08 09:16:38 MarkDuplicates Read 481,000,000 records. Elapsed time: 00:16:12s. Time for last 1,000,000: 1s. Last read position: chr16:31,184,981 INFO 2026-06-08 09:16:38 MarkDuplicates Tracking 480770 as yet unmatched pairs. 37890 records in RAM. INFO 2026-06-08 09:16:40 MarkDuplicates Read 482,000,000 records. Elapsed time: 00:16:14s. Time for last 1,000,000: 2s. Last read position: chr16:31,191,411 INFO 2026-06-08 09:16:40 MarkDuplicates Tracking 479731 as yet unmatched pairs. 36847 records in RAM. INFO 2026-06-08 09:16:42 MarkDuplicates Read 483,000,000 records. Elapsed time: 00:16:16s. Time for last 1,000,000: 2s. Last read position: chr16:50,751,858 INFO 2026-06-08 09:16:42 MarkDuplicates Tracking 475203 as yet unmatched pairs. 32285 records in RAM. INFO 2026-06-08 09:16:44 MarkDuplicates Read 484,000,000 records. Elapsed time: 00:16:18s. Time for last 1,000,000: 1s. Last read position: chr16:53,304,373 INFO 2026-06-08 09:16:44 MarkDuplicates Tracking 473683 as yet unmatched pairs. 30748 records in RAM. INFO 2026-06-08 09:16:46 MarkDuplicates Read 485,000,000 records. Elapsed time: 00:16:20s. Time for last 1,000,000: 2s. Last read position: chr16:57,238,748 INFO 2026-06-08 09:16:46 MarkDuplicates Tracking 470179 as yet unmatched pairs. 27215 records in RAM. INFO 2026-06-08 09:16:48 MarkDuplicates Read 486,000,000 records. Elapsed time: 00:16:22s. Time for last 1,000,000: 1s. Last read position: chr16:66,942,620 INFO 2026-06-08 09:16:48 MarkDuplicates Tracking 467078 as yet unmatched pairs. 24093 records in RAM. INFO 2026-06-08 09:16:50 MarkDuplicates Read 487,000,000 records. Elapsed time: 00:16:24s. Time for last 1,000,000: 2s. Last read position: chr16:67,883,970 INFO 2026-06-08 09:16:50 MarkDuplicates Tracking 463946 as yet unmatched pairs. 20948 records in RAM. INFO 2026-06-08 09:16:52 MarkDuplicates Read 488,000,000 records. Elapsed time: 00:16:26s. Time for last 1,000,000: 1s. Last read position: chr16:69,757,634 INFO 2026-06-08 09:16:52 MarkDuplicates Tracking 460918 as yet unmatched pairs. 17912 records in RAM. INFO 2026-06-08 09:16:54 MarkDuplicates Read 489,000,000 records. Elapsed time: 00:16:28s. Time for last 1,000,000: 2s. Last read position: chr16:71,745,561 INFO 2026-06-08 09:16:54 MarkDuplicates Tracking 458513 as yet unmatched pairs. 15493 records in RAM. INFO 2026-06-08 09:16:56 MarkDuplicates Read 490,000,000 records. Elapsed time: 00:16:30s. Time for last 1,000,000: 2s. Last read position: chr16:72,958,451 INFO 2026-06-08 09:16:56 MarkDuplicates Tracking 455574 as yet unmatched pairs. 12542 records in RAM. INFO 2026-06-08 09:16:57 MarkDuplicates Read 491,000,000 records. Elapsed time: 00:16:31s. Time for last 1,000,000: 1s. Last read position: chr16:81,356,966 INFO 2026-06-08 09:16:57 MarkDuplicates Tracking 452498 as yet unmatched pairs. 9423 records in RAM. INFO 2026-06-08 09:16:59 MarkDuplicates Read 492,000,000 records. Elapsed time: 00:16:33s. Time for last 1,000,000: 2s. Last read position: chr16:88,027,636 INFO 2026-06-08 09:16:59 MarkDuplicates Tracking 449411 as yet unmatched pairs. 6293 records in RAM. INFO 2026-06-08 09:17:01 MarkDuplicates Read 493,000,000 records. Elapsed time: 00:16:35s. Time for last 1,000,000: 1s. Last read position: chr16:89,281,954 INFO 2026-06-08 09:17:01 MarkDuplicates Tracking 446459 as yet unmatched pairs. 3332 records in RAM. INFO 2026-06-08 09:17:05 MarkDuplicates Read 494,000,000 records. Elapsed time: 00:16:39s. Time for last 1,000,000: 3s. Last read position: chr17:517,610 INFO 2026-06-08 09:17:05 MarkDuplicates Tracking 442965 as yet unmatched pairs. 136440 records in RAM. INFO 2026-06-08 09:17:07 MarkDuplicates Read 495,000,000 records. Elapsed time: 00:16:41s. Time for last 1,000,000: 1s. Last read position: chr17:1,593,253 INFO 2026-06-08 09:17:07 MarkDuplicates Tracking 440099 as yet unmatched pairs. 133565 records in RAM. INFO 2026-06-08 09:17:09 MarkDuplicates Read 496,000,000 records. Elapsed time: 00:16:43s. Time for last 1,000,000: 2s. Last read position: chr17:2,058,635 INFO 2026-06-08 09:17:09 MarkDuplicates Tracking 437103 as yet unmatched pairs. 130561 records in RAM. INFO 2026-06-08 09:17:11 MarkDuplicates Read 497,000,000 records. Elapsed time: 00:16:45s. Time for last 1,000,000: 2s. Last read position: chr17:4,552,131 INFO 2026-06-08 09:17:11 MarkDuplicates Tracking 433707 as yet unmatched pairs. 127151 records in RAM. INFO 2026-06-08 09:17:13 MarkDuplicates Read 498,000,000 records. Elapsed time: 00:16:47s. Time for last 1,000,000: 1s. Last read position: chr17:5,486,075 INFO 2026-06-08 09:17:13 MarkDuplicates Tracking 430693 as yet unmatched pairs. 124132 records in RAM. INFO 2026-06-08 09:17:15 MarkDuplicates Read 499,000,000 records. Elapsed time: 00:16:49s. Time for last 1,000,000: 2s. Last read position: chr17:7,311,406 INFO 2026-06-08 09:17:15 MarkDuplicates Tracking 427862 as yet unmatched pairs. 121291 records in RAM. INFO 2026-06-08 09:17:16 MarkDuplicates Read 500,000,000 records. Elapsed time: 00:16:50s. Time for last 1,000,000: 1s. Last read position: chr17:7,513,741 INFO 2026-06-08 09:17:16 MarkDuplicates Tracking 425664 as yet unmatched pairs. 119089 records in RAM. INFO 2026-06-08 09:17:18 MarkDuplicates Read 501,000,000 records. Elapsed time: 00:16:52s. Time for last 1,000,000: 2s. Last read position: chr17:7,849,330 INFO 2026-06-08 09:17:18 MarkDuplicates Tracking 422635 as yet unmatched pairs. 116052 records in RAM. INFO 2026-06-08 09:17:20 MarkDuplicates Read 502,000,000 records. Elapsed time: 00:16:54s. Time for last 1,000,000: 1s. Last read position: chr17:8,150,300 INFO 2026-06-08 09:17:20 MarkDuplicates Tracking 419632 as yet unmatched pairs. 113044 records in RAM. INFO 2026-06-08 09:17:22 MarkDuplicates Read 503,000,000 records. Elapsed time: 00:16:56s. Time for last 1,000,000: 2s. Last read position: chr17:14,236,113 INFO 2026-06-08 09:17:22 MarkDuplicates Tracking 416431 as yet unmatched pairs. 109831 records in RAM. INFO 2026-06-08 09:17:24 MarkDuplicates Read 504,000,000 records. Elapsed time: 00:16:58s. Time for last 1,000,000: 2s. Last read position: chr17:17,158,601 INFO 2026-06-08 09:17:24 MarkDuplicates Tracking 414513 as yet unmatched pairs. 107898 records in RAM. INFO 2026-06-08 09:17:26 MarkDuplicates Read 505,000,000 records. Elapsed time: 00:17:00s. Time for last 1,000,000: 1s. Last read position: chr17:18,603,606 INFO 2026-06-08 09:17:26 MarkDuplicates Tracking 410394 as yet unmatched pairs. 103768 records in RAM. INFO 2026-06-08 09:17:28 MarkDuplicates Read 506,000,000 records. Elapsed time: 00:17:02s. Time for last 1,000,000: 2s. Last read position: chr17:28,598,615 INFO 2026-06-08 09:17:28 MarkDuplicates Tracking 407808 as yet unmatched pairs. 101156 records in RAM. INFO 2026-06-08 09:17:30 MarkDuplicates Read 507,000,000 records. Elapsed time: 00:17:04s. Time for last 1,000,000: 1s. Last read position: chr17:31,226,498 INFO 2026-06-08 09:17:30 MarkDuplicates Tracking 405049 as yet unmatched pairs. 98378 records in RAM. INFO 2026-06-08 09:19:45 MarkDuplicates Read 508,000,000 records. Elapsed time: 00:19:19s. Time for last 1,000,000: 135s. Last read position: chr17:36,384,228 INFO 2026-06-08 09:19:45 MarkDuplicates Tracking 402597 as yet unmatched pairs. 95919 records in RAM. INFO 2026-06-08 09:19:47 MarkDuplicates Read 509,000,000 records. Elapsed time: 00:19:21s. Time for last 1,000,000: 1s. Last read position: chr17:39,201,235 INFO 2026-06-08 09:19:47 MarkDuplicates Tracking 400498 as yet unmatched pairs. 93818 records in RAM. INFO 2026-06-08 09:19:49 MarkDuplicates Read 510,000,000 records. Elapsed time: 00:19:23s. Time for last 1,000,000: 2s. Last read position: chr17:41,690,119 INFO 2026-06-08 09:19:49 MarkDuplicates Tracking 397562 as yet unmatched pairs. 90868 records in RAM. INFO 2026-06-08 09:19:51 MarkDuplicates Read 511,000,000 records. Elapsed time: 00:19:25s. Time for last 1,000,000: 2s. Last read position: chr17:43,529,541 INFO 2026-06-08 09:19:51 MarkDuplicates Tracking 394391 as yet unmatched pairs. 87682 records in RAM. INFO 2026-06-08 09:19:53 MarkDuplicates Read 512,000,000 records. Elapsed time: 00:19:27s. Time for last 1,000,000: 1s. Last read position: chr17:45,515,212 INFO 2026-06-08 09:19:53 MarkDuplicates Tracking 391427 as yet unmatched pairs. 84713 records in RAM. INFO 2026-06-08 09:19:55 MarkDuplicates Read 513,000,000 records. Elapsed time: 00:19:29s. Time for last 1,000,000: 1s. Last read position: chr17:47,838,238 INFO 2026-06-08 09:19:55 MarkDuplicates Tracking 389304 as yet unmatched pairs. 82572 records in RAM. INFO 2026-06-08 09:19:57 MarkDuplicates Read 514,000,000 records. Elapsed time: 00:19:31s. Time for last 1,000,000: 1s. Last read position: chr17:50,185,472 INFO 2026-06-08 09:19:57 MarkDuplicates Tracking 392423 as yet unmatched pairs. 85681 records in RAM. INFO 2026-06-08 09:19:59 MarkDuplicates Read 515,000,000 records. Elapsed time: 00:19:33s. Time for last 1,000,000: 2s. Last read position: chr17:50,186,676 INFO 2026-06-08 09:19:59 MarkDuplicates Tracking 385232 as yet unmatched pairs. 78485 records in RAM. INFO 2026-06-08 09:20:00 MarkDuplicates Read 516,000,000 records. Elapsed time: 00:19:34s. Time for last 1,000,000: 1s. Last read position: chr17:50,187,875 INFO 2026-06-08 09:20:00 MarkDuplicates Tracking 383562 as yet unmatched pairs. 76811 records in RAM. INFO 2026-06-08 09:20:03 MarkDuplicates Read 517,000,000 records. Elapsed time: 00:19:37s. Time for last 1,000,000: 2s. Last read position: chr17:50,188,910 INFO 2026-06-08 09:20:03 MarkDuplicates Tracking 382675 as yet unmatched pairs. 75923 records in RAM. INFO 2026-06-08 09:20:05 MarkDuplicates Read 518,000,000 records. Elapsed time: 00:19:39s. Time for last 1,000,000: 2s. Last read position: chr17:50,189,685 INFO 2026-06-08 09:20:05 MarkDuplicates Tracking 385626 as yet unmatched pairs. 78867 records in RAM. INFO 2026-06-08 09:20:07 MarkDuplicates Read 519,000,000 records. Elapsed time: 00:19:41s. Time for last 1,000,000: 1s. Last read position: chr17:50,190,877 INFO 2026-06-08 09:20:07 MarkDuplicates Tracking 373490 as yet unmatched pairs. 66727 records in RAM. INFO 2026-06-08 09:20:09 MarkDuplicates Read 520,000,000 records. Elapsed time: 00:19:43s. Time for last 1,000,000: 2s. Last read position: chr17:50,192,998 INFO 2026-06-08 09:20:09 MarkDuplicates Tracking 372215 as yet unmatched pairs. 65441 records in RAM. INFO 2026-06-08 09:20:11 MarkDuplicates Read 521,000,000 records. Elapsed time: 00:19:45s. Time for last 1,000,000: 1s. Last read position: chr17:50,194,592 INFO 2026-06-08 09:20:11 MarkDuplicates Tracking 367067 as yet unmatched pairs. 60277 records in RAM. INFO 2026-06-08 09:20:13 MarkDuplicates Read 522,000,000 records. Elapsed time: 00:19:47s. Time for last 1,000,000: 2s. Last read position: chr17:50,195,629 INFO 2026-06-08 09:20:13 MarkDuplicates Tracking 366389 as yet unmatched pairs. 59594 records in RAM. INFO 2026-06-08 09:20:15 MarkDuplicates Read 523,000,000 records. Elapsed time: 00:19:49s. Time for last 1,000,000: 2s. Last read position: chr17:50,196,644 INFO 2026-06-08 09:20:15 MarkDuplicates Tracking 361912 as yet unmatched pairs. 55110 records in RAM. INFO 2026-06-08 09:20:17 MarkDuplicates Read 524,000,000 records. Elapsed time: 00:19:51s. Time for last 1,000,000: 1s. Last read position: chr17:50,198,464 INFO 2026-06-08 09:20:17 MarkDuplicates Tracking 357884 as yet unmatched pairs. 51077 records in RAM. INFO 2026-06-08 09:20:19 MarkDuplicates Read 525,000,000 records. Elapsed time: 00:19:53s. Time for last 1,000,000: 2s. Last read position: chr17:50,199,770 INFO 2026-06-08 09:20:19 MarkDuplicates Tracking 355203 as yet unmatched pairs. 48395 records in RAM. INFO 2026-06-08 09:20:21 MarkDuplicates Read 526,000,000 records. Elapsed time: 00:19:55s. Time for last 1,000,000: 1s. Last read position: chr17:50,750,793 INFO 2026-06-08 09:20:21 MarkDuplicates Tracking 348082 as yet unmatched pairs. 41257 records in RAM. INFO 2026-06-08 09:20:23 MarkDuplicates Read 527,000,000 records. Elapsed time: 00:19:57s. Time for last 1,000,000: 2s. Last read position: chr17:59,211,382 INFO 2026-06-08 09:20:23 MarkDuplicates Tracking 344411 as yet unmatched pairs. 37561 records in RAM. INFO 2026-06-08 09:20:25 MarkDuplicates Read 528,000,000 records. Elapsed time: 00:19:59s. Time for last 1,000,000: 2s. Last read position: chr17:59,878,152 INFO 2026-06-08 09:20:25 MarkDuplicates Tracking 341714 as yet unmatched pairs. 34853 records in RAM. INFO 2026-06-08 09:20:27 MarkDuplicates Read 529,000,000 records. Elapsed time: 00:20:01s. Time for last 1,000,000: 1s. Last read position: chr17:63,421,808 INFO 2026-06-08 09:20:27 MarkDuplicates Tracking 338801 as yet unmatched pairs. 31931 records in RAM. INFO 2026-06-08 09:20:29 MarkDuplicates Read 530,000,000 records. Elapsed time: 00:20:03s. Time for last 1,000,000: 2s. Last read position: chr17:64,578,567 INFO 2026-06-08 09:20:29 MarkDuplicates Tracking 335832 as yet unmatched pairs. 28953 records in RAM. INFO 2026-06-08 09:20:30 MarkDuplicates Read 531,000,000 records. Elapsed time: 00:20:04s. Time for last 1,000,000: 1s. Last read position: chr17:68,035,809 INFO 2026-06-08 09:20:30 MarkDuplicates Tracking 333451 as yet unmatched pairs. 26558 records in RAM. INFO 2026-06-08 09:20:32 MarkDuplicates Read 532,000,000 records. Elapsed time: 00:20:06s. Time for last 1,000,000: 2s. Last read position: chr17:69,027,802 INFO 2026-06-08 09:20:32 MarkDuplicates Tracking 330689 as yet unmatched pairs. 23790 records in RAM. INFO 2026-06-08 09:20:35 MarkDuplicates Read 533,000,000 records. Elapsed time: 00:20:09s. Time for last 1,000,000: 2s. Last read position: chr17:75,003,915 INFO 2026-06-08 09:20:35 MarkDuplicates Tracking 327878 as yet unmatched pairs. 20945 records in RAM. INFO 2026-06-08 09:20:36 MarkDuplicates Read 534,000,000 records. Elapsed time: 00:20:10s. Time for last 1,000,000: 1s. Last read position: chr17:75,778,602 INFO 2026-06-08 09:20:36 MarkDuplicates Tracking 325882 as yet unmatched pairs. 18942 records in RAM. INFO 2026-06-08 09:20:38 MarkDuplicates Read 535,000,000 records. Elapsed time: 00:20:12s. Time for last 1,000,000: 2s. Last read position: chr17:76,775,121 INFO 2026-06-08 09:20:38 MarkDuplicates Tracking 321487 as yet unmatched pairs. 14542 records in RAM. INFO 2026-06-08 09:20:40 MarkDuplicates Read 536,000,000 records. Elapsed time: 00:20:14s. Time for last 1,000,000: 1s. Last read position: chr17:79,080,948 INFO 2026-06-08 09:20:40 MarkDuplicates Tracking 318505 as yet unmatched pairs. 11541 records in RAM. INFO 2026-06-08 09:20:42 MarkDuplicates Read 537,000,000 records. Elapsed time: 00:20:16s. Time for last 1,000,000: 2s. Last read position: chr17:81,251,542 INFO 2026-06-08 09:20:42 MarkDuplicates Tracking 315213 as yet unmatched pairs. 8235 records in RAM. INFO 2026-06-08 09:20:44 MarkDuplicates Read 538,000,000 records. Elapsed time: 00:20:18s. Time for last 1,000,000: 1s. Last read position: chr17:81,846,591 INFO 2026-06-08 09:20:44 MarkDuplicates Tracking 311850 as yet unmatched pairs. 4861 records in RAM. INFO 2026-06-08 09:20:46 MarkDuplicates Read 539,000,000 records. Elapsed time: 00:20:20s. Time for last 1,000,000: 2s. Last read position: chr17:82,458,707 INFO 2026-06-08 09:20:46 MarkDuplicates Tracking 308269 as yet unmatched pairs. 1266 records in RAM. INFO 2026-06-08 09:20:48 MarkDuplicates Read 540,000,000 records. Elapsed time: 00:20:22s. Time for last 1,000,000: 2s. Last read position: chr18:3,457,421 INFO 2026-06-08 09:20:48 MarkDuplicates Tracking 305450 as yet unmatched pairs. 20154 records in RAM. INFO 2026-06-08 09:20:50 MarkDuplicates Read 541,000,000 records. Elapsed time: 00:20:24s. Time for last 1,000,000: 1s. Last read position: chr18:13,056,253 INFO 2026-06-08 09:20:50 MarkDuplicates Tracking 302935 as yet unmatched pairs. 17629 records in RAM. INFO 2026-06-08 09:20:52 MarkDuplicates Read 542,000,000 records. Elapsed time: 00:20:26s. Time for last 1,000,000: 2s. Last read position: chr18:26,274,718 INFO 2026-06-08 09:20:52 MarkDuplicates Tracking 299948 as yet unmatched pairs. 14621 records in RAM. INFO 2026-06-08 09:20:54 MarkDuplicates Read 543,000,000 records. Elapsed time: 00:20:28s. Time for last 1,000,000: 1s. Last read position: chr18:44,869,241 INFO 2026-06-08 09:20:54 MarkDuplicates Tracking 297755 as yet unmatched pairs. 12399 records in RAM. INFO 2026-06-08 09:20:56 MarkDuplicates Read 544,000,000 records. Elapsed time: 00:20:30s. Time for last 1,000,000: 1s. Last read position: chr18:49,333,728 INFO 2026-06-08 09:20:56 MarkDuplicates Tracking 295400 as yet unmatched pairs. 10018 records in RAM. INFO 2026-06-08 09:20:58 MarkDuplicates Read 545,000,000 records. Elapsed time: 00:20:32s. Time for last 1,000,000: 1s. Last read position: chr18:55,279,577 INFO 2026-06-08 09:20:58 MarkDuplicates Tracking 293411 as yet unmatched pairs. 8016 records in RAM. INFO 2026-06-08 09:21:00 MarkDuplicates Read 546,000,000 records. Elapsed time: 00:20:34s. Time for last 1,000,000: 2s. Last read position: chr18:62,154,641 INFO 2026-06-08 09:21:00 MarkDuplicates Tracking 289865 as yet unmatched pairs. 4455 records in RAM. INFO 2026-06-08 09:21:02 MarkDuplicates Read 547,000,000 records. Elapsed time: 00:20:36s. Time for last 1,000,000: 2s. Last read position: chr18:76,959,728 INFO 2026-06-08 09:21:02 MarkDuplicates Tracking 286558 as yet unmatched pairs. 1136 records in RAM. INFO 2026-06-08 09:21:04 MarkDuplicates Read 548,000,000 records. Elapsed time: 00:20:38s. Time for last 1,000,000: 2s. Last read position: chr19:1,010,855 INFO 2026-06-08 09:21:04 MarkDuplicates Tracking 283180 as yet unmatched pairs. 99864 records in RAM. INFO 2026-06-08 09:21:07 MarkDuplicates Read 549,000,000 records. Elapsed time: 00:20:41s. Time for last 1,000,000: 2s. Last read position: chr19:1,417,499 INFO 2026-06-08 09:21:07 MarkDuplicates Tracking 279840 as yet unmatched pairs. 96516 records in RAM. INFO 2026-06-08 09:21:08 MarkDuplicates Read 550,000,000 records. Elapsed time: 00:20:42s. Time for last 1,000,000: 1s. Last read position: chr19:2,121,776 INFO 2026-06-08 09:21:08 MarkDuplicates Tracking 276050 as yet unmatched pairs. 92721 records in RAM. INFO 2026-06-08 09:21:10 MarkDuplicates Read 551,000,000 records. Elapsed time: 00:20:44s. Time for last 1,000,000: 2s. Last read position: chr19:3,027,858 INFO 2026-06-08 09:21:10 MarkDuplicates Tracking 273600 as yet unmatched pairs. 90268 records in RAM. INFO 2026-06-08 09:21:12 MarkDuplicates Read 552,000,000 records. Elapsed time: 00:20:46s. Time for last 1,000,000: 1s. Last read position: chr19:4,475,523 INFO 2026-06-08 09:21:12 MarkDuplicates Tracking 269167 as yet unmatched pairs. 85829 records in RAM. INFO 2026-06-08 09:21:14 MarkDuplicates Read 553,000,000 records. Elapsed time: 00:20:48s. Time for last 1,000,000: 2s. Last read position: chr19:5,661,694 INFO 2026-06-08 09:21:14 MarkDuplicates Tracking 266044 as yet unmatched pairs. 82698 records in RAM. INFO 2026-06-08 09:21:16 MarkDuplicates Read 554,000,000 records. Elapsed time: 00:20:50s. Time for last 1,000,000: 2s. Last read position: chr19:7,519,253 INFO 2026-06-08 09:21:16 MarkDuplicates Tracking 262632 as yet unmatched pairs. 79279 records in RAM. INFO 2026-06-08 09:21:18 MarkDuplicates Read 555,000,000 records. Elapsed time: 00:20:52s. Time for last 1,000,000: 1s. Last read position: chr19:9,380,054 INFO 2026-06-08 09:21:18 MarkDuplicates Tracking 259463 as yet unmatched pairs. 76103 records in RAM. INFO 2026-06-08 09:21:20 MarkDuplicates Read 556,000,000 records. Elapsed time: 00:20:54s. Time for last 1,000,000: 2s. Last read position: chr19:10,333,367 INFO 2026-06-08 09:21:20 MarkDuplicates Tracking 256380 as yet unmatched pairs. 73017 records in RAM. INFO 2026-06-08 09:21:22 MarkDuplicates Read 557,000,000 records. Elapsed time: 00:20:56s. Time for last 1,000,000: 1s. Last read position: chr19:11,003,032 INFO 2026-06-08 09:21:22 MarkDuplicates Tracking 253463 as yet unmatched pairs. 70093 records in RAM. INFO 2026-06-08 09:21:24 MarkDuplicates Read 558,000,000 records. Elapsed time: 00:20:58s. Time for last 1,000,000: 1s. Last read position: chr19:11,948,981 INFO 2026-06-08 09:21:24 MarkDuplicates Tracking 250622 as yet unmatched pairs. 67249 records in RAM. INFO 2026-06-08 09:21:26 MarkDuplicates Read 559,000,000 records. Elapsed time: 00:21:00s. Time for last 1,000,000: 1s. Last read position: chr19:13,025,164 INFO 2026-06-08 09:21:26 MarkDuplicates Tracking 248571 as yet unmatched pairs. 65192 records in RAM. INFO 2026-06-08 09:21:28 MarkDuplicates Read 560,000,000 records. Elapsed time: 00:21:02s. Time for last 1,000,000: 2s. Last read position: chr19:14,093,683 INFO 2026-06-08 09:21:28 MarkDuplicates Tracking 244146 as yet unmatched pairs. 60763 records in RAM. INFO 2026-06-08 09:21:30 MarkDuplicates Read 561,000,000 records. Elapsed time: 00:21:04s. Time for last 1,000,000: 2s. Last read position: chr19:15,179,262 INFO 2026-06-08 09:21:30 MarkDuplicates Tracking 240628 as yet unmatched pairs. 57239 records in RAM. INFO 2026-06-08 09:21:32 MarkDuplicates Read 562,000,000 records. Elapsed time: 00:21:06s. Time for last 1,000,000: 1s. Last read position: chr19:15,253,603 INFO 2026-06-08 09:21:32 MarkDuplicates Tracking 238731 as yet unmatched pairs. 55328 records in RAM. INFO 2026-06-08 09:21:34 MarkDuplicates Read 563,000,000 records. Elapsed time: 00:21:08s. Time for last 1,000,000: 2s. Last read position: chr19:15,427,127 INFO 2026-06-08 09:21:34 MarkDuplicates Tracking 234892 as yet unmatched pairs. 51486 records in RAM. INFO 2026-06-08 09:21:35 MarkDuplicates Read 564,000,000 records. Elapsed time: 00:21:09s. Time for last 1,000,000: 1s. Last read position: chr19:17,162,987 INFO 2026-06-08 09:21:35 MarkDuplicates Tracking 231471 as yet unmatched pairs. 48057 records in RAM. INFO 2026-06-08 09:21:37 MarkDuplicates Read 565,000,000 records. Elapsed time: 00:21:11s. Time for last 1,000,000: 2s. Last read position: chr19:18,280,581 INFO 2026-06-08 09:21:37 MarkDuplicates Tracking 228436 as yet unmatched pairs. 45013 records in RAM. INFO 2026-06-08 09:21:39 MarkDuplicates Read 566,000,000 records. Elapsed time: 00:21:13s. Time for last 1,000,000: 1s. Last read position: chr19:18,777,310 INFO 2026-06-08 09:21:39 MarkDuplicates Tracking 224825 as yet unmatched pairs. 41402 records in RAM. INFO 2026-06-08 09:21:41 MarkDuplicates Read 567,000,000 records. Elapsed time: 00:21:15s. Time for last 1,000,000: 2s. Last read position: chr19:21,116,844 INFO 2026-06-08 09:21:41 MarkDuplicates Tracking 221772 as yet unmatched pairs. 38328 records in RAM. INFO 2026-06-08 09:21:43 MarkDuplicates Read 568,000,000 records. Elapsed time: 00:21:17s. Time for last 1,000,000: 2s. Last read position: chr19:35,009,176 INFO 2026-06-08 09:21:43 MarkDuplicates Tracking 219095 as yet unmatched pairs. 35639 records in RAM. INFO 2026-06-08 09:21:45 MarkDuplicates Read 569,000,000 records. Elapsed time: 00:21:19s. Time for last 1,000,000: 1s. Last read position: chr19:38,383,299 INFO 2026-06-08 09:21:45 MarkDuplicates Tracking 215747 as yet unmatched pairs. 32284 records in RAM. INFO 2026-06-08 09:21:47 MarkDuplicates Read 570,000,000 records. Elapsed time: 00:21:21s. Time for last 1,000,000: 2s. Last read position: chr19:39,433,676 INFO 2026-06-08 09:21:47 MarkDuplicates Tracking 213327 as yet unmatched pairs. 29850 records in RAM. INFO 2026-06-08 09:21:49 MarkDuplicates Read 571,000,000 records. Elapsed time: 00:21:23s. Time for last 1,000,000: 1s. Last read position: chr19:41,305,641 INFO 2026-06-08 09:21:49 MarkDuplicates Tracking 209826 as yet unmatched pairs. 26344 records in RAM. INFO 2026-06-08 09:21:51 MarkDuplicates Read 572,000,000 records. Elapsed time: 00:21:25s. Time for last 1,000,000: 1s. Last read position: chr19:42,297,065 INFO 2026-06-08 09:21:51 MarkDuplicates Tracking 206645 as yet unmatched pairs. 23160 records in RAM. INFO 2026-06-08 09:21:53 MarkDuplicates Read 573,000,000 records. Elapsed time: 00:21:27s. Time for last 1,000,000: 1s. Last read position: chr19:45,472,558 INFO 2026-06-08 09:21:53 MarkDuplicates Tracking 203734 as yet unmatched pairs. 20223 records in RAM. INFO 2026-06-08 09:21:55 MarkDuplicates Read 574,000,000 records. Elapsed time: 00:21:29s. Time for last 1,000,000: 1s. Last read position: chr19:46,921,523 INFO 2026-06-08 09:21:55 MarkDuplicates Tracking 200006 as yet unmatched pairs. 16491 records in RAM. INFO 2026-06-08 09:21:57 MarkDuplicates Read 575,000,000 records. Elapsed time: 00:21:31s. Time for last 1,000,000: 2s. Last read position: chr19:48,961,586 INFO 2026-06-08 09:21:57 MarkDuplicates Tracking 196869 as yet unmatched pairs. 13348 records in RAM. INFO 2026-06-08 09:21:59 MarkDuplicates Read 576,000,000 records. Elapsed time: 00:21:33s. Time for last 1,000,000: 1s. Last read position: chr19:49,802,031 INFO 2026-06-08 09:21:59 MarkDuplicates Tracking 193718 as yet unmatched pairs. 10190 records in RAM. INFO 2026-06-08 09:22:01 MarkDuplicates Read 577,000,000 records. Elapsed time: 00:21:35s. Time for last 1,000,000: 2s. Last read position: chr19:53,109,442 INFO 2026-06-08 09:22:01 MarkDuplicates Tracking 190716 as yet unmatched pairs. 7185 records in RAM. INFO 2026-06-08 09:22:02 MarkDuplicates Read 578,000,000 records. Elapsed time: 00:21:36s. Time for last 1,000,000: 1s. Last read position: chr19:55,517,914 INFO 2026-06-08 09:22:02 MarkDuplicates Tracking 187618 as yet unmatched pairs. 4080 records in RAM. INFO 2026-06-08 09:22:04 MarkDuplicates Read 579,000,000 records. Elapsed time: 00:21:38s. Time for last 1,000,000: 1s. Last read position: chr19:58,127,875 INFO 2026-06-08 09:22:04 MarkDuplicates Tracking 184731 as yet unmatched pairs. 1182 records in RAM. INFO 2026-06-08 09:22:07 MarkDuplicates Read 580,000,000 records. Elapsed time: 00:21:41s. Time for last 1,000,000: 2s. Last read position: chr20:2,794,420 INFO 2026-06-08 09:22:07 MarkDuplicates Tracking 181541 as yet unmatched pairs. 42987 records in RAM. INFO 2026-06-08 09:22:09 MarkDuplicates Read 581,000,000 records. Elapsed time: 00:21:43s. Time for last 1,000,000: 2s. Last read position: chr20:3,963,887 INFO 2026-06-08 09:22:09 MarkDuplicates Tracking 178559 as yet unmatched pairs. 39998 records in RAM. INFO 2026-06-08 09:22:11 MarkDuplicates Read 582,000,000 records. Elapsed time: 00:21:45s. Time for last 1,000,000: 2s. Last read position: chr20:16,738,886 INFO 2026-06-08 09:22:11 MarkDuplicates Tracking 175429 as yet unmatched pairs. 36857 records in RAM. INFO 2026-06-08 09:22:12 MarkDuplicates Read 583,000,000 records. Elapsed time: 00:21:46s. Time for last 1,000,000: 1s. Last read position: chr20:21,162,965 INFO 2026-06-08 09:22:12 MarkDuplicates Tracking 172928 as yet unmatched pairs. 34346 records in RAM. INFO 2026-06-08 09:22:14 MarkDuplicates Read 584,000,000 records. Elapsed time: 00:21:48s. Time for last 1,000,000: 2s. Last read position: chr20:32,436,625 INFO 2026-06-08 09:22:14 MarkDuplicates Tracking 170034 as yet unmatched pairs. 31440 records in RAM. INFO 2026-06-08 09:22:16 MarkDuplicates Read 585,000,000 records. Elapsed time: 00:21:50s. Time for last 1,000,000: 1s. Last read position: chr20:35,280,758 INFO 2026-06-08 09:22:16 MarkDuplicates Tracking 167018 as yet unmatched pairs. 28420 records in RAM. INFO 2026-06-08 09:22:18 MarkDuplicates Read 586,000,000 records. Elapsed time: 00:21:52s. Time for last 1,000,000: 2s. Last read position: chr20:36,805,853 INFO 2026-06-08 09:22:18 MarkDuplicates Tracking 164177 as yet unmatched pairs. 25577 records in RAM. INFO 2026-06-08 09:22:20 MarkDuplicates Read 587,000,000 records. Elapsed time: 00:21:54s. Time for last 1,000,000: 2s. Last read position: chr20:41,163,927 INFO 2026-06-08 09:22:20 MarkDuplicates Tracking 161545 as yet unmatched pairs. 22942 records in RAM. INFO 2026-06-08 09:22:22 MarkDuplicates Read 588,000,000 records. Elapsed time: 00:21:56s. Time for last 1,000,000: 1s. Last read position: chr20:43,513,512 INFO 2026-06-08 09:22:22 MarkDuplicates Tracking 158263 as yet unmatched pairs. 19649 records in RAM. INFO 2026-06-08 09:22:24 MarkDuplicates Read 589,000,000 records. Elapsed time: 00:21:58s. Time for last 1,000,000: 2s. Last read position: chr20:47,246,439 INFO 2026-06-08 09:22:24 MarkDuplicates Tracking 155266 as yet unmatched pairs. 16647 records in RAM. INFO 2026-06-08 09:22:26 MarkDuplicates Read 590,000,000 records. Elapsed time: 00:22:00s. Time for last 1,000,000: 1s. Last read position: chr20:51,432,276 INFO 2026-06-08 09:22:26 MarkDuplicates Tracking 152383 as yet unmatched pairs. 13755 records in RAM. INFO 2026-06-08 09:22:28 MarkDuplicates Read 591,000,000 records. Elapsed time: 00:22:02s. Time for last 1,000,000: 1s. Last read position: chr20:57,488,964 INFO 2026-06-08 09:22:28 MarkDuplicates Tracking 149595 as yet unmatched pairs. 10956 records in RAM. INFO 2026-06-08 09:22:30 MarkDuplicates Read 592,000,000 records. Elapsed time: 00:22:04s. Time for last 1,000,000: 1s. Last read position: chr20:58,895,659 INFO 2026-06-08 09:22:30 MarkDuplicates Tracking 147843 as yet unmatched pairs. 9193 records in RAM. INFO 2026-06-08 09:22:32 MarkDuplicates Read 593,000,000 records. Elapsed time: 00:22:06s. Time for last 1,000,000: 2s. Last read position: chr20:62,813,465 INFO 2026-06-08 09:22:32 MarkDuplicates Tracking 142939 as yet unmatched pairs. 4280 records in RAM. INFO 2026-06-08 09:22:34 MarkDuplicates Read 594,000,000 records. Elapsed time: 00:22:08s. Time for last 1,000,000: 2s. Last read position: chr20:63,963,780 INFO 2026-06-08 09:22:34 MarkDuplicates Tracking 139425 as yet unmatched pairs. 758 records in RAM. INFO 2026-06-08 09:22:36 MarkDuplicates Read 595,000,000 records. Elapsed time: 00:22:10s. Time for last 1,000,000: 1s. Last read position: chr21:8,218,124 INFO 2026-06-08 09:22:36 MarkDuplicates Tracking 137373 as yet unmatched pairs. 26422 records in RAM. INFO 2026-06-08 09:22:37 MarkDuplicates Read 596,000,000 records. Elapsed time: 00:22:11s. Time for last 1,000,000: 1s. Last read position: chr21:8,399,905 INFO 2026-06-08 09:22:37 MarkDuplicates Tracking 136827 as yet unmatched pairs. 25870 records in RAM. INFO 2026-06-08 09:22:38 MarkDuplicates Read 597,000,000 records. Elapsed time: 00:22:12s. Time for last 1,000,000: 1s. Last read position: chr21:8,988,016 INFO 2026-06-08 09:22:38 MarkDuplicates Tracking 135473 as yet unmatched pairs. 24512 records in RAM. INFO 2026-06-08 09:22:40 MarkDuplicates Read 598,000,000 records. Elapsed time: 00:22:14s. Time for last 1,000,000: 1s. Last read position: chr21:32,325,248 INFO 2026-06-08 09:22:40 MarkDuplicates Tracking 132789 as yet unmatched pairs. 21818 records in RAM. INFO 2026-06-08 09:22:42 MarkDuplicates Read 599,000,000 records. Elapsed time: 00:22:16s. Time for last 1,000,000: 1s. Last read position: chr21:33,575,786 INFO 2026-06-08 09:22:42 MarkDuplicates Tracking 130018 as yet unmatched pairs. 19042 records in RAM. INFO 2026-06-08 09:22:44 MarkDuplicates Read 600,000,000 records. Elapsed time: 00:22:18s. Time for last 1,000,000: 2s. Last read position: chr21:37,185,710 INFO 2026-06-08 09:22:44 MarkDuplicates Tracking 127289 as yet unmatched pairs. 16313 records in RAM. INFO 2026-06-08 09:22:46 MarkDuplicates Read 601,000,000 records. Elapsed time: 00:22:20s. Time for last 1,000,000: 2s. Last read position: chr21:43,565,504 INFO 2026-06-08 09:22:46 MarkDuplicates Tracking 124417 as yet unmatched pairs. 13426 records in RAM. INFO 2026-06-08 09:22:48 MarkDuplicates Read 602,000,000 records. Elapsed time: 00:22:22s. Time for last 1,000,000: 1s. Last read position: chr21:45,986,595 INFO 2026-06-08 09:22:48 MarkDuplicates Tracking 121857 as yet unmatched pairs. 10859 records in RAM. INFO 2026-06-08 09:22:50 MarkDuplicates Read 603,000,000 records. Elapsed time: 00:22:24s. Time for last 1,000,000: 2s. Last read position: chr21:46,002,003 INFO 2026-06-08 09:22:50 MarkDuplicates Tracking 118826 as yet unmatched pairs. 7823 records in RAM. INFO 2026-06-08 09:22:52 MarkDuplicates Read 604,000,000 records. Elapsed time: 00:22:26s. Time for last 1,000,000: 1s. Last read position: chr21:46,121,091 INFO 2026-06-08 09:22:52 MarkDuplicates Tracking 115240 as yet unmatched pairs. 4229 records in RAM. INFO 2026-06-08 09:22:54 MarkDuplicates Read 605,000,000 records. Elapsed time: 00:22:28s. Time for last 1,000,000: 2s. Last read position: chr22:11,707,210 INFO 2026-06-08 09:22:54 MarkDuplicates Tracking 111035 as yet unmatched pairs. 44162 records in RAM. INFO 2026-06-08 09:22:56 MarkDuplicates Read 606,000,000 records. Elapsed time: 00:22:30s. Time for last 1,000,000: 1s. Last read position: chr22:20,126,357 INFO 2026-06-08 09:22:56 MarkDuplicates Tracking 108044 as yet unmatched pairs. 41169 records in RAM. INFO 2026-06-08 09:22:58 MarkDuplicates Read 607,000,000 records. Elapsed time: 00:22:32s. Time for last 1,000,000: 1s. Last read position: chr22:21,720,012 INFO 2026-06-08 09:22:58 MarkDuplicates Tracking 104847 as yet unmatched pairs. 37970 records in RAM. INFO 2026-06-08 09:23:00 MarkDuplicates Read 608,000,000 records. Elapsed time: 00:22:34s. Time for last 1,000,000: 1s. Last read position: chr22:23,973,167 INFO 2026-06-08 09:23:00 MarkDuplicates Tracking 101590 as yet unmatched pairs. 34710 records in RAM. INFO 2026-06-08 09:23:02 MarkDuplicates Read 609,000,000 records. Elapsed time: 00:22:36s. Time for last 1,000,000: 1s. Last read position: chr22:27,983,355 INFO 2026-06-08 09:23:02 MarkDuplicates Tracking 98751 as yet unmatched pairs. 31869 records in RAM. INFO 2026-06-08 09:23:04 MarkDuplicates Read 610,000,000 records. Elapsed time: 00:22:38s. Time for last 1,000,000: 1s. Last read position: chr22:29,287,030 INFO 2026-06-08 09:23:04 MarkDuplicates Tracking 96340 as yet unmatched pairs. 29454 records in RAM. INFO 2026-06-08 09:23:06 MarkDuplicates Read 611,000,000 records. Elapsed time: 00:22:40s. Time for last 1,000,000: 1s. Last read position: chr22:30,020,434 INFO 2026-06-08 09:23:06 MarkDuplicates Tracking 92726 as yet unmatched pairs. 25840 records in RAM. INFO 2026-06-08 09:23:08 MarkDuplicates Read 612,000,000 records. Elapsed time: 00:22:42s. Time for last 1,000,000: 2s. Last read position: chr22:32,479,104 INFO 2026-06-08 09:23:08 MarkDuplicates Tracking 89690 as yet unmatched pairs. 22799 records in RAM. INFO 2026-06-08 09:23:09 MarkDuplicates Read 613,000,000 records. Elapsed time: 00:22:43s. Time for last 1,000,000: 1s. Last read position: chr22:37,614,234 INFO 2026-06-08 09:23:09 MarkDuplicates Tracking 86349 as yet unmatched pairs. 19453 records in RAM. INFO 2026-06-08 09:23:11 MarkDuplicates Read 614,000,000 records. Elapsed time: 00:22:45s. Time for last 1,000,000: 1s. Last read position: chr22:38,300,785 INFO 2026-06-08 09:23:11 MarkDuplicates Tracking 83612 as yet unmatched pairs. 16714 records in RAM. INFO 2026-06-08 09:23:13 MarkDuplicates Read 615,000,000 records. Elapsed time: 00:22:47s. Time for last 1,000,000: 2s. Last read position: chr22:39,521,524 INFO 2026-06-08 09:23:13 MarkDuplicates Tracking 80545 as yet unmatched pairs. 13641 records in RAM. INFO 2026-06-08 09:23:15 MarkDuplicates Read 616,000,000 records. Elapsed time: 00:22:49s. Time for last 1,000,000: 1s. Last read position: chr22:41,149,920 INFO 2026-06-08 09:23:15 MarkDuplicates Tracking 77635 as yet unmatched pairs. 10730 records in RAM. INFO 2026-06-08 09:23:17 MarkDuplicates Read 617,000,000 records. Elapsed time: 00:22:51s. Time for last 1,000,000: 1s. Last read position: chr22:42,210,442 INFO 2026-06-08 09:23:17 MarkDuplicates Tracking 74734 as yet unmatched pairs. 7828 records in RAM. INFO 2026-06-08 09:23:19 MarkDuplicates Read 618,000,000 records. Elapsed time: 00:22:53s. Time for last 1,000,000: 1s. Last read position: chr22:49,823,651 INFO 2026-06-08 09:23:19 MarkDuplicates Tracking 71848 as yet unmatched pairs. 4936 records in RAM. INFO 2026-06-08 09:23:21 MarkDuplicates Read 619,000,000 records. Elapsed time: 00:22:55s. Time for last 1,000,000: 2s. Last read position: chr22:50,503,633 INFO 2026-06-08 09:23:21 MarkDuplicates Tracking 68280 as yet unmatched pairs. 1368 records in RAM. INFO 2026-06-08 09:23:24 MarkDuplicates Read 620,000,000 records. Elapsed time: 00:22:58s. Time for last 1,000,000: 2s. Last read position: chrX:3,320,785 INFO 2026-06-08 09:23:24 MarkDuplicates Tracking 65034 as yet unmatched pairs. 53248 records in RAM. INFO 2026-06-08 09:23:25 MarkDuplicates Read 621,000,000 records. Elapsed time: 00:22:59s. Time for last 1,000,000: 1s. Last read position: chrX:14,244,444 INFO 2026-06-08 09:23:25 MarkDuplicates Tracking 62055 as yet unmatched pairs. 50269 records in RAM. INFO 2026-06-08 09:23:27 MarkDuplicates Read 622,000,000 records. Elapsed time: 00:23:01s. Time for last 1,000,000: 2s. Last read position: chrX:30,855,232 INFO 2026-06-08 09:23:27 MarkDuplicates Tracking 59685 as yet unmatched pairs. 47865 records in RAM. INFO 2026-06-08 09:23:29 MarkDuplicates Read 623,000,000 records. Elapsed time: 00:23:03s. Time for last 1,000,000: 1s. Last read position: chrX:41,343,725 INFO 2026-06-08 09:23:29 MarkDuplicates Tracking 57137 as yet unmatched pairs. 45314 records in RAM. INFO 2026-06-08 09:23:31 MarkDuplicates Read 624,000,000 records. Elapsed time: 00:23:05s. Time for last 1,000,000: 2s. Last read position: chrX:47,585,647 INFO 2026-06-08 09:23:31 MarkDuplicates Tracking 54453 as yet unmatched pairs. 42626 records in RAM. INFO 2026-06-08 09:23:33 MarkDuplicates Read 625,000,000 records. Elapsed time: 00:23:07s. Time for last 1,000,000: 1s. Last read position: chrX:50,090,232 INFO 2026-06-08 09:23:33 MarkDuplicates Tracking 50916 as yet unmatched pairs. 39088 records in RAM. INFO 2026-06-08 09:23:35 MarkDuplicates Read 626,000,000 records. Elapsed time: 00:23:09s. Time for last 1,000,000: 1s. Last read position: chrX:53,086,026 INFO 2026-06-08 09:23:35 MarkDuplicates Tracking 48781 as yet unmatched pairs. 36952 records in RAM. INFO 2026-06-08 09:23:37 MarkDuplicates Read 627,000,000 records. Elapsed time: 00:23:11s. Time for last 1,000,000: 1s. Last read position: chrX:53,615,781 INFO 2026-06-08 09:23:37 MarkDuplicates Tracking 45980 as yet unmatched pairs. 34151 records in RAM. INFO 2026-06-08 09:23:39 MarkDuplicates Read 628,000,000 records. Elapsed time: 00:23:13s. Time for last 1,000,000: 2s. Last read position: chrX:64,900,867 INFO 2026-06-08 09:23:39 MarkDuplicates Tracking 42762 as yet unmatched pairs. 30932 records in RAM. INFO 2026-06-08 09:23:41 MarkDuplicates Read 629,000,000 records. Elapsed time: 00:23:15s. Time for last 1,000,000: 2s. Last read position: chrX:71,290,656 INFO 2026-06-08 09:23:41 MarkDuplicates Tracking 40218 as yet unmatched pairs. 28387 records in RAM. INFO 2026-06-08 09:23:43 MarkDuplicates Read 630,000,000 records. Elapsed time: 00:23:17s. Time for last 1,000,000: 1s. Last read position: chrX:72,273,861 INFO 2026-06-08 09:23:43 MarkDuplicates Tracking 37776 as yet unmatched pairs. 25945 records in RAM. INFO 2026-06-08 09:23:45 MarkDuplicates Read 631,000,000 records. Elapsed time: 00:23:19s. Time for last 1,000,000: 2s. Last read position: chrX:77,683,288 INFO 2026-06-08 09:23:45 MarkDuplicates Tracking 36374 as yet unmatched pairs. 24542 records in RAM. INFO 2026-06-08 09:23:46 MarkDuplicates Read 632,000,000 records. Elapsed time: 00:23:20s. Time for last 1,000,000: 1s. Last read position: chrX:100,406,768 INFO 2026-06-08 09:23:46 MarkDuplicates Tracking 32181 as yet unmatched pairs. 20346 records in RAM. INFO 2026-06-08 09:23:48 MarkDuplicates Read 633,000,000 records. Elapsed time: 00:23:22s. Time for last 1,000,000: 1s. Last read position: chrX:103,972,891 INFO 2026-06-08 09:23:48 MarkDuplicates Tracking 29562 as yet unmatched pairs. 17727 records in RAM. INFO 2026-06-08 09:23:50 MarkDuplicates Read 634,000,000 records. Elapsed time: 00:23:24s. Time for last 1,000,000: 2s. Last read position: chrX:111,410,210 INFO 2026-06-08 09:23:50 MarkDuplicates Tracking 27022 as yet unmatched pairs. 15187 records in RAM. INFO 2026-06-08 09:23:52 MarkDuplicates Read 635,000,000 records. Elapsed time: 00:23:26s. Time for last 1,000,000: 1s. Last read position: chrX:123,665,642 INFO 2026-06-08 09:23:52 MarkDuplicates Tracking 24373 as yet unmatched pairs. 12538 records in RAM. INFO 2026-06-08 09:23:54 MarkDuplicates Read 636,000,000 records. Elapsed time: 00:23:28s. Time for last 1,000,000: 2s. Last read position: chrX:133,622,717 INFO 2026-06-08 09:23:54 MarkDuplicates Tracking 21697 as yet unmatched pairs. 9862 records in RAM. INFO 2026-06-08 09:23:56 MarkDuplicates Read 637,000,000 records. Elapsed time: 00:23:30s. Time for last 1,000,000: 1s. Last read position: chrX:151,226,638 INFO 2026-06-08 09:23:56 MarkDuplicates Tracking 19043 as yet unmatched pairs. 7205 records in RAM. INFO 2026-06-08 09:23:58 MarkDuplicates Read 638,000,000 records. Elapsed time: 00:23:32s. Time for last 1,000,000: 1s. Last read position: chrX:154,348,791 INFO 2026-06-08 09:23:58 MarkDuplicates Tracking 16238 as yet unmatched pairs. 4400 records in RAM. INFO 2026-06-08 09:24:00 MarkDuplicates Read 639,000,000 records. Elapsed time: 00:23:34s. Time for last 1,000,000: 1s. Last read position: chrX:154,487,502 INFO 2026-06-08 09:24:00 MarkDuplicates Tracking 12719 as yet unmatched pairs. 881 records in RAM. INFO 2026-06-08 09:24:02 MarkDuplicates Read 640,000,000 records. Elapsed time: 00:23:36s. Time for last 1,000,000: 1s. Last read position: chrY:22,724,737 INFO 2026-06-08 09:24:02 MarkDuplicates Tracking 10360 as yet unmatched pairs. 97 records in RAM. INFO 2026-06-08 09:24:03 MarkDuplicates Read 641,000,000 records. Elapsed time: 00:23:37s. Time for last 1,000,000: 1s. Last read position: GL000220.1:116,795 INFO 2026-06-08 09:24:03 MarkDuplicates Tracking 7925 as yet unmatched pairs. 134 records in RAM. INFO 2026-06-08 09:24:05 MarkDuplicates Read 642,000,000 records. Elapsed time: 00:23:39s. Time for last 1,000,000: 1s. Last read position: KI270711.1:26,391 INFO 2026-06-08 09:24:05 MarkDuplicates Tracking 7673 as yet unmatched pairs. 111 records in RAM. INFO 2026-06-08 09:24:06 MarkDuplicates Read 643,000,000 records. Elapsed time: 00:23:40s. Time for last 1,000,000: 1s. Last read position: KI270733.1:171,318 INFO 2026-06-08 09:24:06 MarkDuplicates Tracking 378 as yet unmatched pairs. 285 records in RAM. INFO 2026-06-08 09:24:07 MarkDuplicates Read 643879957 records. 0 pairs never matched. INFO 2026-06-08 09:24:51 MarkDuplicates After buildSortedReadEndLists freeMemory: 57969338688; totalMemory: 82778783744; maxMemory: 127137742848 INFO 2026-06-08 09:24:51 MarkDuplicates Will retain up to 2147483642 duplicate indices before spilling to disk. INFO 2026-06-08 09:24:53 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2026-06-08 09:25:14 OpticalDuplicateFinder Large duplicate set. size = 1262 INFO 2026-06-08 09:25:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:28,247 INFO 2026-06-08 09:25:18 OpticalDuplicateFinder Large duplicate set. size = 1009 INFO 2026-06-08 09:25:18 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:12,617 INFO 2026-06-08 09:25:20 OpticalDuplicateFinder Large duplicate set. size = 1694 INFO 2026-06-08 09:25:20 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:7,965 INFO 2026-06-08 09:25:23 OpticalDuplicateFinder Large duplicate set. size = 1056 INFO 2026-06-08 09:25:23 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:27,268 INFO 2026-06-08 09:25:26 OpticalDuplicateFinder Large duplicate set. size = 1071 INFO 2026-06-08 09:25:26 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-27,751 INFO 2026-06-08 09:25:27 OpticalDuplicateFinder Large duplicate set. size = 2118 INFO 2026-06-08 09:25:27 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-18,811 INFO 2026-06-08 09:25:27 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:16,662 INFO 2026-06-08 09:25:27 OpticalDuplicateFinder Large duplicate set. size = 1271 INFO 2026-06-08 09:25:27 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:22,147 INFO 2026-06-08 09:25:28 OpticalDuplicateFinder Large duplicate set. size = 1184 INFO 2026-06-08 09:25:28 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:2,149 INFO 2026-06-08 09:25:28 OpticalDuplicateFinder Large duplicate set. size = 1025 INFO 2026-06-08 09:25:28 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-28,204 INFO 2026-06-08 09:25:28 OpticalDuplicateFinder Large duplicate set. size = 1001 INFO 2026-06-08 09:25:28 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:27,009 INFO 2026-06-08 09:25:28 OpticalDuplicateFinder Large duplicate set. size = 1288 INFO 2026-06-08 09:25:28 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-29,045 INFO 2026-06-08 09:25:33 OpticalDuplicateFinder Large duplicate set. size = 1364 INFO 2026-06-08 09:25:33 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:5,142 INFO 2026-06-08 09:25:33 OpticalDuplicateFinder Large duplicate set. size = 1931 INFO 2026-06-08 09:25:33 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:26,055 INFO 2026-06-08 09:25:33 OpticalDuplicateFinder Large duplicate set. size = 1544 INFO 2026-06-08 09:25:33 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:17,989 INFO 2026-06-08 09:25:33 OpticalDuplicateFinder Large duplicate set. size = 1157 INFO 2026-06-08 09:25:33 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:30,262 INFO 2026-06-08 09:25:36 OpticalDuplicateFinder Large duplicate set. size = 2062 INFO 2026-06-08 09:25:36 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:15,691 INFO 2026-06-08 09:25:36 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:8,847 INFO 2026-06-08 09:25:40 OpticalDuplicateFinder Large duplicate set. size = 1014 INFO 2026-06-08 09:25:40 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:4,794 INFO 2026-06-08 09:25:43 OpticalDuplicateFinder Large duplicate set. size = 1061 INFO 2026-06-08 09:25:43 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:22,010 INFO 2026-06-08 09:25:45 OpticalDuplicateFinder Large duplicate set. size = 1022 INFO 2026-06-08 09:25:45 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:29,113 INFO 2026-06-08 09:25:45 OpticalDuplicateFinder Large duplicate set. size = 1177 INFO 2026-06-08 09:25:45 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:5,830 INFO 2026-06-08 09:25:45 OpticalDuplicateFinder Large duplicate set. size = 1370 INFO 2026-06-08 09:25:45 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-20,963 INFO 2026-06-08 09:25:45 OpticalDuplicateFinder Large duplicate set. size = 1171 INFO 2026-06-08 09:25:45 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:14,268 INFO 2026-06-08 09:25:45 OpticalDuplicateFinder Large duplicate set. size = 1184 INFO 2026-06-08 09:25:45 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:13,871 INFO 2026-06-08 09:25:45 OpticalDuplicateFinder Large duplicate set. size = 1209 INFO 2026-06-08 09:25:45 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-20,801 INFO 2026-06-08 09:25:45 OpticalDuplicateFinder Large duplicate set. size = 1318 INFO 2026-06-08 09:25:45 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-20,915 INFO 2026-06-08 09:25:45 OpticalDuplicateFinder Large duplicate set. size = 1106 INFO 2026-06-08 09:25:45 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-25,631 INFO 2026-06-08 09:25:45 OpticalDuplicateFinder Large duplicate set. size = 1124 INFO 2026-06-08 09:25:45 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:29,008 INFO 2026-06-08 09:25:45 OpticalDuplicateFinder Large duplicate set. size = 1117 INFO 2026-06-08 09:25:45 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:20,764 INFO 2026-06-08 09:25:46 OpticalDuplicateFinder Large duplicate set. size = 1078 INFO 2026-06-08 09:25:46 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-14,920 INFO 2026-06-08 09:25:46 OpticalDuplicateFinder Large duplicate set. size = 1006 INFO 2026-06-08 09:25:46 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:11,137 INFO 2026-06-08 09:25:46 OpticalDuplicateFinder Large duplicate set. size = 1006 INFO 2026-06-08 09:25:46 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-31,068 INFO 2026-06-08 09:25:46 OpticalDuplicateFinder Large duplicate set. size = 1849 INFO 2026-06-08 09:25:46 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:8,030 INFO 2026-06-08 09:25:46 OpticalDuplicateFinder Large duplicate set. size = 1236 INFO 2026-06-08 09:25:46 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:18,523 INFO 2026-06-08 09:25:46 OpticalDuplicateFinder Large duplicate set. size = 1133 INFO 2026-06-08 09:25:46 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:4,365 INFO 2026-06-08 09:25:46 OpticalDuplicateFinder Large duplicate set. size = 1786 INFO 2026-06-08 09:25:46 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-17,485 INFO 2026-06-08 09:25:46 OpticalDuplicateFinder Large duplicate set. size = 2277 INFO 2026-06-08 09:25:46 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:1,777 INFO 2026-06-08 09:25:46 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-26,820 INFO 2026-06-08 09:25:46 OpticalDuplicateFinder Large duplicate set. size = 1222 INFO 2026-06-08 09:25:46 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:18,749 INFO 2026-06-08 09:25:46 OpticalDuplicateFinder Large duplicate set. size = 1129 INFO 2026-06-08 09:25:46 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:9,503 INFO 2026-06-08 09:25:46 OpticalDuplicateFinder Large duplicate set. size = 1001 INFO 2026-06-08 09:25:46 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-21,829 INFO 2026-06-08 09:25:46 OpticalDuplicateFinder Large duplicate set. size = 1158 INFO 2026-06-08 09:25:46 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-15,122 INFO 2026-06-08 09:25:46 OpticalDuplicateFinder Large duplicate set. size = 1435 INFO 2026-06-08 09:25:46 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:25,772 INFO 2026-06-08 09:25:46 OpticalDuplicateFinder Large duplicate set. size = 1475 INFO 2026-06-08 09:25:46 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:11,857 INFO 2026-06-08 09:25:46 OpticalDuplicateFinder Large duplicate set. size = 1092 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:12,464 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder Large duplicate set. size = 1602 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-18,180 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder Large duplicate set. size = 2444 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:9,033 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:10,894 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder Large duplicate set. size = 1020 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:10,037 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder Large duplicate set. size = 2130 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:30,051 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:12,981 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder Large duplicate set. size = 1544 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-19,782 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder Large duplicate set. size = 1698 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-26,497 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder Large duplicate set. size = 1062 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:16,193 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder Large duplicate set. size = 1264 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-22,743 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder Large duplicate set. size = 1419 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-29,611 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder Large duplicate set. size = 1158 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-18,116 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder Large duplicate set. size = 1405 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:26,726 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder Large duplicate set. size = 2342 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-18,237 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-31,480 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder Large duplicate set. size = 3786 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:4,867 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:16,177 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder compared 3,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:30,795 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder Large duplicate set. size = 1331 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:8,168 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder Large duplicate set. size = 1688 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-19,240 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder Large duplicate set. size = 1985 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:18,855 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder Large duplicate set. size = 1645 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-24,782 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder Large duplicate set. size = 1292 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:9,122 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder Large duplicate set. size = 1254 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:6,064 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder Large duplicate set. size = 1098 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-16,538 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder Large duplicate set. size = 1732 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:20,262 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder Large duplicate set. size = 1113 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:31,637 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder Large duplicate set. size = 1029 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-31,949 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder Large duplicate set. size = 1507 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-26,893 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder Large duplicate set. size = 2034 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:27,333 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-23,406 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder Large duplicate set. size = 1038 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-18,059 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder Large duplicate set. size = 1257 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-16,328 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder Large duplicate set. size = 1123 INFO 2026-06-08 09:25:47 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-30,962 INFO 2026-06-08 09:25:48 OpticalDuplicateFinder Large duplicate set. size = 1299 INFO 2026-06-08 09:25:48 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-20,963 INFO 2026-06-08 09:25:49 OpticalDuplicateFinder Large duplicate set. size = 1070 INFO 2026-06-08 09:25:49 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-31,286 INFO 2026-06-08 09:26:13 MarkDuplicates Traversing fragment information and detecting duplicates. WARNING 2026-06-08 09:26:13 SortingCollection There is not enough memory per file for buffering. Reading will be unbuffered. INFO 2026-06-08 09:27:39 MarkDuplicates Sorting list of duplicate records. INFO 2026-06-08 09:27:40 MarkDuplicates After generateDuplicateIndexes freeMemory: 203920424; totalMemory: 234881024; maxMemory: 127137742848 INFO 2026-06-08 09:27:40 MarkDuplicates Marking 282933335 records as duplicates. INFO 2026-06-08 09:27:40 MarkDuplicates Found 7021324 optical duplicate clusters. INFO 2026-06-08 09:27:40 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2026-06-08 09:27:56 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:16s. Time for last 10,000,000: 16s. Last read position: chr1:25,563,117 INFO 2026-06-08 09:28:12 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:32s. Time for last 10,000,000: 15s. Last read position: chr1:46,034,222 INFO 2026-06-08 09:28:28 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:00:48s. Time for last 10,000,000: 16s. Last read position: chr1:116,961,415 INFO 2026-06-08 09:28:44 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:04s. Time for last 10,000,000: 16s. Last read position: chr1:149,886,425 INFO 2026-06-08 09:29:00 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:01:20s. Time for last 10,000,000: 15s. Last read position: chr1:171,524,920 INFO 2026-06-08 09:29:17 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:01:36s. Time for last 10,000,000: 16s. Last read position: chr1:225,856,955 INFO 2026-06-08 09:29:33 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:01:53s. Time for last 10,000,000: 16s. Last read position: chr2:32,916,253 INFO 2026-06-08 09:29:50 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:02:09s. Time for last 10,000,000: 16s. Last read position: chr2:55,317,818 INFO 2026-06-08 09:30:06 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:02:25s. Time for last 10,000,000: 16s. Last read position: chr2:108,764,300 INFO 2026-06-08 09:30:22 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:02:42s. Time for last 10,000,000: 16s. Last read position: chr2:178,621,574 INFO 2026-06-08 09:30:38 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:02:58s. Time for last 10,000,000: 16s. Last read position: chr2:215,435,723 INFO 2026-06-08 09:30:54 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:03:14s. Time for last 10,000,000: 16s. Last read position: chr3:15,432,199 INFO 2026-06-08 09:31:10 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:03:30s. Time for last 10,000,000: 16s. Last read position: chr3:53,228,303 INFO 2026-06-08 09:31:27 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:03:46s. Time for last 10,000,000: 16s. Last read position: chr3:184,321,764 INFO 2026-06-08 09:31:43 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:04:03s. Time for last 10,000,000: 16s. Last read position: chr4:56,988,134 INFO 2026-06-08 09:31:59 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:04:19s. Time for last 10,000,000: 16s. Last read position: chr4:151,099,697 INFO 2026-06-08 09:32:15 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:04:35s. Time for last 10,000,000: 16s. Last read position: chr5:65,795,420 INFO 2026-06-08 09:32:31 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:04:51s. Time for last 10,000,000: 16s. Last read position: chr5:136,160,965 INFO 2026-06-08 09:32:46 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:05:06s. Time for last 10,000,000: 15s. Last read position: chr5:142,314,997 INFO 2026-06-08 09:33:02 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:05:22s. Time for last 10,000,000: 15s. Last read position: chr5:179,614,887 INFO 2026-06-08 09:33:18 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:05:38s. Time for last 10,000,000: 15s. Last read position: chr6:32,035,184 INFO 2026-06-08 09:33:34 MarkDuplicates Written 220,000,000 records. Elapsed time: 00:05:54s. Time for last 10,000,000: 16s. Last read position: chr6:87,524,616 INFO 2026-06-08 09:33:50 MarkDuplicates Written 230,000,000 records. Elapsed time: 00:06:10s. Time for last 10,000,000: 16s. Last read position: chr6:160,096,501 INFO 2026-06-08 09:34:07 MarkDuplicates Written 240,000,000 records. Elapsed time: 00:06:26s. Time for last 10,000,000: 16s. Last read position: chr7:44,106,772 INFO 2026-06-08 09:34:23 MarkDuplicates Written 250,000,000 records. Elapsed time: 00:06:42s. Time for last 10,000,000: 15s. Last read position: chr7:94,404,874 INFO 2026-06-08 09:34:38 MarkDuplicates Written 260,000,000 records. Elapsed time: 00:06:58s. Time for last 10,000,000: 15s. Last read position: chr7:127,707,599 INFO 2026-06-08 09:34:55 MarkDuplicates Written 270,000,000 records. Elapsed time: 00:07:14s. Time for last 10,000,000: 16s. Last read position: chr8:22,606,140 INFO 2026-06-08 09:35:11 MarkDuplicates Written 280,000,000 records. Elapsed time: 00:07:30s. Time for last 10,000,000: 15s. Last read position: chr8:73,257,075 INFO 2026-06-08 09:35:27 MarkDuplicates Written 290,000,000 records. Elapsed time: 00:07:46s. Time for last 10,000,000: 15s. Last read position: chr9:713,068 INFO 2026-06-08 09:35:43 MarkDuplicates Written 300,000,000 records. Elapsed time: 00:08:02s. Time for last 10,000,000: 16s. Last read position: chr9:93,660,228 INFO 2026-06-08 09:35:59 MarkDuplicates Written 310,000,000 records. Elapsed time: 00:08:18s. Time for last 10,000,000: 15s. Last read position: chr9:130,885,173 INFO 2026-06-08 09:36:14 MarkDuplicates Written 320,000,000 records. Elapsed time: 00:08:34s. Time for last 10,000,000: 15s. Last read position: chr10:58,702,087 INFO 2026-06-08 09:36:30 MarkDuplicates Written 330,000,000 records. Elapsed time: 00:08:50s. Time for last 10,000,000: 15s. Last read position: chr11:2,132,956 INFO 2026-06-08 09:36:46 MarkDuplicates Written 340,000,000 records. Elapsed time: 00:09:06s. Time for last 10,000,000: 16s. Last read position: chr11:57,811,460 INFO 2026-06-08 09:37:02 MarkDuplicates Written 350,000,000 records. Elapsed time: 00:09:22s. Time for last 10,000,000: 15s. Last read position: chr11:69,005,866 INFO 2026-06-08 09:37:19 MarkDuplicates Written 360,000,000 records. Elapsed time: 00:09:38s. Time for last 10,000,000: 16s. Last read position: chr11:119,419,493 INFO 2026-06-08 09:37:34 MarkDuplicates Written 370,000,000 records. Elapsed time: 00:09:54s. Time for last 10,000,000: 15s. Last read position: chr12:14,882,178 INFO 2026-06-08 09:37:50 MarkDuplicates Written 380,000,000 records. Elapsed time: 00:10:10s. Time for last 10,000,000: 15s. Last read position: chr12:55,716,088 INFO 2026-06-08 09:38:06 MarkDuplicates Written 390,000,000 records. Elapsed time: 00:10:26s. Time for last 10,000,000: 15s. Last read position: chr12:89,349,348 INFO 2026-06-08 09:38:22 MarkDuplicates Written 400,000,000 records. Elapsed time: 00:10:42s. Time for last 10,000,000: 15s. Last read position: chr12:131,932,184 INFO 2026-06-08 09:38:38 MarkDuplicates Written 410,000,000 records. Elapsed time: 00:10:58s. Time for last 10,000,000: 16s. Last read position: chr13:95,589,156 INFO 2026-06-08 09:38:54 MarkDuplicates Written 420,000,000 records. Elapsed time: 00:11:14s. Time for last 10,000,000: 15s. Last read position: chr14:35,123,521 INFO 2026-06-08 09:39:10 MarkDuplicates Written 430,000,000 records. Elapsed time: 00:11:30s. Time for last 10,000,000: 16s. Last read position: chr14:92,026,865 INFO 2026-06-08 09:39:26 MarkDuplicates Written 440,000,000 records. Elapsed time: 00:11:46s. Time for last 10,000,000: 16s. Last read position: chr15:42,351,366 INFO 2026-06-08 09:39:42 MarkDuplicates Written 450,000,000 records. Elapsed time: 00:12:02s. Time for last 10,000,000: 16s. Last read position: chr15:75,490,209 INFO 2026-06-08 09:39:58 MarkDuplicates Written 460,000,000 records. Elapsed time: 00:12:18s. Time for last 10,000,000: 15s. Last read position: chr16:2,115,597 INFO 2026-06-08 09:40:14 MarkDuplicates Written 470,000,000 records. Elapsed time: 00:12:34s. Time for last 10,000,000: 15s. Last read position: chr16:18,364,253 INFO 2026-06-08 09:40:30 MarkDuplicates Written 480,000,000 records. Elapsed time: 00:12:50s. Time for last 10,000,000: 15s. Last read position: chr16:30,782,005 INFO 2026-06-08 09:40:46 MarkDuplicates Written 490,000,000 records. Elapsed time: 00:13:06s. Time for last 10,000,000: 15s. Last read position: chr16:72,958,451 INFO 2026-06-08 09:41:02 MarkDuplicates Written 500,000,000 records. Elapsed time: 00:13:22s. Time for last 10,000,000: 15s. Last read position: chr17:7,513,741 INFO 2026-06-08 09:41:18 MarkDuplicates Written 510,000,000 records. Elapsed time: 00:13:37s. Time for last 10,000,000: 15s. Last read position: chr17:41,690,119 INFO 2026-06-08 09:41:33 MarkDuplicates Written 520,000,000 records. Elapsed time: 00:13:53s. Time for last 10,000,000: 15s. Last read position: chr17:50,192,998 INFO 2026-06-08 09:41:49 MarkDuplicates Written 530,000,000 records. Elapsed time: 00:14:09s. Time for last 10,000,000: 15s. Last read position: chr17:64,578,567 INFO 2026-06-08 09:42:05 MarkDuplicates Written 540,000,000 records. Elapsed time: 00:14:25s. Time for last 10,000,000: 16s. Last read position: chr18:3,457,421 INFO 2026-06-08 09:42:21 MarkDuplicates Written 550,000,000 records. Elapsed time: 00:14:41s. Time for last 10,000,000: 16s. Last read position: chr19:2,121,776 INFO 2026-06-08 09:42:37 MarkDuplicates Written 560,000,000 records. Elapsed time: 00:14:57s. Time for last 10,000,000: 15s. Last read position: chr19:14,093,683 INFO 2026-06-08 09:42:53 MarkDuplicates Written 570,000,000 records. Elapsed time: 00:15:12s. Time for last 10,000,000: 15s. Last read position: chr19:39,433,676 INFO 2026-06-08 09:43:09 MarkDuplicates Written 580,000,000 records. Elapsed time: 00:15:28s. Time for last 10,000,000: 15s. Last read position: chr20:2,794,420 INFO 2026-06-08 09:43:25 MarkDuplicates Written 590,000,000 records. Elapsed time: 00:15:44s. Time for last 10,000,000: 16s. Last read position: chr20:51,432,276 INFO 2026-06-08 09:43:40 MarkDuplicates Written 600,000,000 records. Elapsed time: 00:16:00s. Time for last 10,000,000: 15s. Last read position: chr21:37,185,710 INFO 2026-06-08 09:43:56 MarkDuplicates Written 610,000,000 records. Elapsed time: 00:16:15s. Time for last 10,000,000: 15s. Last read position: chr22:29,287,030 INFO 2026-06-08 09:44:12 MarkDuplicates Written 620,000,000 records. Elapsed time: 00:16:31s. Time for last 10,000,000: 15s. Last read position: chrX:3,320,785 INFO 2026-06-08 09:44:28 MarkDuplicates Written 630,000,000 records. Elapsed time: 00:16:47s. Time for last 10,000,000: 15s. Last read position: chrX:72,273,861 INFO 2026-06-08 09:44:44 MarkDuplicates Written 640,000,000 records. Elapsed time: 00:17:03s. Time for last 10,000,000: 16s. Last read position: chrY:22,724,737 INFO 2026-06-08 09:45:00 MarkDuplicates Writing complete. Closing input iterator. INFO 2026-06-08 09:45:00 MarkDuplicates Duplicate Index cleanup. INFO 2026-06-08 09:45:00 MarkDuplicates Getting Memory Stats. INFO 2026-06-08 09:45:00 MarkDuplicates Before output close freeMemory: 203907168; totalMemory: 234881024; maxMemory: 127137742848 INFO 2026-06-08 09:45:00 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2026-06-08 09:45:00 MarkDuplicates After output close freeMemory: 104133920; totalMemory: 134217728; maxMemory: 127137742848 [Mon Jun 08 09:45:00 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 44.62 minutes. Runtime.totalMemory()=134217728 Tool returned: 0 ls: *cram: No such file or directory ls: *.crai: No such file or directory